I uploaded a minimal working example, it's a stripped down version of a
> book, text removed apart from a stub using greek text (Unicode
> capabilities), the prologue is intact, the default font is Tinos, a freely
> downloadable font, but if you want you can substitute it with
> LiberationSerif or any other font that supports polytonic Greek.
>

Thanks for this. I used LiberationSerif font which is by default shipped
with Ubuntu.

These are the warnings, I get:


LaTeX Font Warning: Font shape `EU1/LiberationSerif(0)/m/sl' undefined
(Font)              using `EU1/LiberationSerif(0)/m/n' instead on input
line 43
.

LaTeX Font Warning: Some font shapes were not available, defaults
substituted.

Which I believe is perfectly normal and you ought to get the same warnings
with TeXLive 2010. This happens because Italic or oblique  version of
LiberationSerif does not exist and so fontspec uses the regular shape of
the font for slanted shape (produced by \textsl, etc).


 Please provide me with an example for pdflatex, I don't know how to use it
> :)
>

What I meant was that you produce a similar example with pdflatex (no
polyglossia, no fontspec, no xelatex specific packages) and see if the same
issue happens.

Please download this version of fontspec (from 2010) and put it in your
current directory, does the problem still exists?

http://tug.org/svn/texlive/trunk/Master/texmf-dist/tex/latex/fontspec/fontspec.sty?revision=18558&view=co

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