Hi.

> > I tried the attached source with TL2013 pretest, then the attached PDF 
> > (ipaexm-jp90-test-TL2013.pdf) was produced.
> > The PDF contains three glyphs and all these glyphs should be same (see 
> > ipaexm-jp90-test-TL2012.pdf, which is generated by TL2012).
> > But the first and second glyphs are different from the third glyph.
> > The fontspec package output the following warnings:
>
> Your test file runs fine here. Can you post your logfile?

I attach the log file.

Best regards
Kazuki Maeda
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. Defining document command \setmathrm with arg. spec. 'O{}m' on line 68.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \setboldmathrm with arg. spec. 'O{}m' on line 72.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \setmathsf with arg. spec. 'O{}m' on line 76.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \setmathtt with arg. spec. 'O{}m' on line 80.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newfontfamily with arg. spec. 'mO{}m' on line 99.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newfontface with arg. spec. 'mO{}m' on line 103.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \defaultfontfeatures with arg. spec. 'om' on line
. 111.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \addfontfeatures with arg. spec. 'm' on line 147.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newfontfeature with arg. spec. 'mm' on line 159.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newAATfeature with arg. spec. 'mmmm' on line 167.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newICUfeature with arg. spec. 'mmm' on line 175.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \aliasfontfeature with arg. spec. 'mm' on line
. 204.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \aliasfontfeatureoption with arg. spec. 'mmm' on
. line 206.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newfontscript with arg. spec. 'mm' on line 211.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \newfontlanguage with arg. spec. 'mm' on line 238.
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. LaTeX info: "xparse/define-command"
. 
. Defining document command \DeclareFontsExtensions with arg. spec. 'm' on
. line 259.
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Variant \prop_gput:cnV already defined; not changing it on line 586
Variant \prop_gput:cnx already defined; not changing it on line 587
\l_fontspec_tmp_int=\count317
LaTeX Info: Redefining \itshape on input line 2012.
LaTeX Info: Redefining \slshape on input line 2017.
LaTeX Info: Redefining \scshape on input line 2022.
LaTeX Info: Redefining \upshape on input line 2027.

(/usr/local/texlive/2013/texmf-dist/tex/latex/fontspec/fontspec.cfg)))
(./ipaexm-jp90-test.aux)
LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for EU2/lmr/m/n on input line 3.
LaTeX Font Info:    ... okay on input line 3.
LaTeX Font Info:    Checking defaults for T3/cmr/m/n on input line 3.
LaTeX Font Info:    Try loading font information for T3+cmr on input line 3.

(/usr/local/texlive/2013/texmf-dist/tex/latex/tipa/t3cmr.fd
File: t3cmr.fd 2001/12/31 TIPA font definitions
)
LaTeX Font Info:    ... okay on input line 3.

(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count318
\scratchdimen=\dimen292
\scratchbox=\box271
\nofMPsegments=\count319
\nofMParguments=\count320
\everyMPshowfont=\toks18
\MPscratchCnt=\count321
\MPscratchDim=\dimen293
\MPnumerator=\count322
\makeMPintoPDFobject=\count323
\everyMPtoPDFconversion=\toks19
) (/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf

(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/grfext.sty
Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)

(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty
Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
))
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty
Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)

(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)

(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/etexcmds.sty
Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
)))
Package grfext Info: Graphics extension search list:
(grfext)             [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPEG
,.JBIG2,.JB2,.eps]
(grfext)             \AppendGraphicsExtensions on input line 452.

(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Live

))
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. fontspec info: "setup-math"
. 
. Adjusting the maths setup (use [no-math] to avoid this).
.................................................
\symlegacymaths=\mathgroup4
LaTeX Font Info:    Overwriting symbol font `legacymaths' in version `bold'
(Font)                  OT1/cmr/m/n --> OT1/cmr/bx/n on input line 3.
LaTeX Font Info:    Redeclaring math accent \acute on input line 3.
LaTeX Font Info:    Redeclaring math accent \grave on input line 3.
LaTeX Font Info:    Redeclaring math accent \ddot on input line 3.
LaTeX Font Info:    Redeclaring math accent \tilde on input line 3.
LaTeX Font Info:    Redeclaring math accent \bar on input line 3.
LaTeX Font Info:    Redeclaring math accent \breve on input line 3.
LaTeX Font Info:    Redeclaring math accent \check on input line 3.
LaTeX Font Info:    Redeclaring math accent \hat on input line 3.
LaTeX Font Info:    Redeclaring math accent \dot on input line 3.
LaTeX Font Info:    Redeclaring math accent \mathring on input line 3.
LaTeX Font Info:    Redeclaring math symbol \colon on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Gamma on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Delta on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Theta on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Lambda on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Xi on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Pi on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Sigma on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Upsilon on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Phi on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Psi on input line 3.
LaTeX Font Info:    Redeclaring math symbol \Omega on input line 3.
LaTeX Font Info:    Redeclaring math symbol \mathdollar on input line 3.
LaTeX Font Info:    Redeclaring symbol font `operators' on input line 3.
LaTeX Font Info:    Encoding `OT1' has changed to `EU2' for symbol font
(Font)              `operators' in the math version `normal' on input line 3.
LaTeX Font Info:    Overwriting symbol font `operators' in version `normal'
(Font)                  OT1/cmr/m/n --> EU2/lmr/m/n on input line 3.
LaTeX Font Info:    Encoding `OT1' has changed to `EU2' for symbol font
(Font)              `operators' in the math version `bold' on input line 3.
LaTeX Font Info:    Overwriting symbol font `operators' in version `bold'
(Font)                  OT1/cmr/bx/n --> EU2/lmr/m/n on input line 3.
LaTeX Font Info:    Overwriting symbol font `operators' in version `normal'
(Font)                  EU2/lmr/m/n --> EU2/lmr/m/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathrm' in version `normal'
(Font)                  EU2/lmr/m/n --> EU2/lmr/m/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathit' in version `normal'
(Font)                  OT1/cmr/m/it --> EU2/lmr/m/it on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathbf' in version `normal'
(Font)                  OT1/cmr/bx/n --> EU2/lmr/bx/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathsf' in version `normal'
(Font)                  OT1/cmss/m/n --> EU2/lmss/m/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathtt' in version `normal'
(Font)                  OT1/cmtt/m/n --> EU2/lmtt/m/n on input line 3.
LaTeX Font Info:    Overwriting symbol font `operators' in version `bold'
(Font)                  EU2/lmr/m/n --> EU2/lmr/bx/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathrm' in version `bold'
(Font)                  EU2/lmr/m/n --> EU2/lmr/bx/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathit' in version `bold'
(Font)                  OT1/cmr/bx/it --> EU2/lmr/bx/it on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathsf' in version `bold'
(Font)                  OT1/cmss/bx/n --> EU2/lmss/bx/n on input line 3.
LaTeX Font Info:    Overwriting math alphabet `\mathtt' in version `bold'
(Font)                  OT1/cmtt/m/n --> EU2/lmtt/bx/n on input line 3.
\g__file_internal_ior=\read1
luaotfload | load: auto-selecting default features for script: dflt(load luc: /h
ome/kmaeda/.texlive2013/texmf-var/luatex-cache/generic/fonts/otf/ipaexm.luc)
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-scripts"
. 
. Font IPAexMincho does not contain any OpenType `Script' information.
.................................................

*************************************************
* fontspec warning: "icu-feature-not-exist-in-font"
* 
* OpenType feature 'CJKShape=JIS1990' (+jp90) not available for font
* 'IPAexMincho' with script '' and language ''.
*************************************************
\g_fontspec_family_IPAexMincho_int=\count324
luaotfload | load: auto-selecting default features for script: dflt
*************************************************
* fontspec warning: "icu-feature-not-exist-in-font"
* 
* OpenType feature 'CJKShape=JIS1990' (+jp90) not available for font
* 'IPAexMincho' with script '' and language ''.
*************************************************
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/B (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/I (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/BI (it probably doesn't exist).
.................................................
.................................................
. fontspec info: "defining-font"
. 
. Font family 'IPAexMincho(0)' created for font 'IPAexMincho' with options
. [CJKShape=JIS1990].
. 
. This font family consists of the following shapes:
. 
. * 'normal' with NFSS spec.:
. <->"name:IPAexMincho:mode=node;"
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-scripts"
. 
. Font IPAexMincho does not contain any OpenType `Script' information.
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/B (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/I (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/BI (it probably doesn't exist).
.................................................
.................................................
. fontspec info: "defining-font"
. 
. Font family 'IPAexMincho(1)' created for font 'IPAexMincho' with options
. [RawFeature={+jp90}].
. 
. This font family consists of the following shapes:
. 
. * 'normal' with NFSS spec.:
. <->"name:IPAexMincho:mode=node;+jp90;"
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-scripts"
. 
. Font IPAexMincho does not contain any OpenType `Script' information.
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/B (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/I (it probably doesn't exist).
.................................................
luaotfload | load: auto-selecting default features for script: dflt
luaotfload | load: auto-selecting default features for script: dflt
.................................................
. fontspec info: "no-font-shape"
. 
. Could not resolve font IPAexMincho/BI (it probably doesn't exist).
.................................................
.................................................
. fontspec info: "defining-font"
. 
. Font family 'IPAexMincho(2)' created for font 'IPAexMincho' with options
. [RawFeature={script=latn;+jp90}].
. 
. This font family consists of the following shapes:
. 
. * 'normal' with NFSS spec.:
. <->"name:IPAexMincho:mode=node;script=latn;+jp90;"
.................................................
luaotfload | load: auto-selecting default features for script: latn
luaotfload | load: no defaults for script “latn”, falling back to “dflt
” [1

{/usr/local/texlive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(./ipaexm-jp90-test.aux) )

Here is how much of LuaTeX's memory you used:
 15174 strings out of 494719
 100000,383344 words of node,token memory allocated
 293 words of node memory still in use:
   3 hlist, 1 vlist, 1 rule, 2 glue, 3 attribute, 42 glue_spec, 3 attribute_list
, 1 write nodes
   avail lists: 2:23,3:2,4:26,6:10,7:1,9:6
 18423 multiletter control sequences out of 65536+600000
 24 fonts using 8841247 bytes
 48i,4n,46p,373b,175s stack positions out of 5000i,500n,10000p,200000b,100000s
</usr/share/fonts/tex/opentype/public/lm/lmroman10-regular.otf></usr/local/texli
ve/2013/texmf-dist/fonts/truetype/public/ipaex/ipaexm.ttf>
Output written on ipaexm-jp90-test.pdf (1 page, 153389 bytes).

PDF statistics: 22 PDF objects out of 1000 (max. 8388607)
 12 compressed objects within 1 object stream
 0 named destinations out of 1000 (max. 131072)
 1 words of extra memory for PDF output out of 10000 (max. 10000000)

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