I have been sitting on this one for some time, and today I did some tests. The problem was introduced somewhere between 5.2.10 and 5.3 and it can easily be inferred where it is happening in the process by comparing the pdftex log part of the log files below.
I can provide the log files or more examples. I have versions 5.3.11 to .14 that I could experiment with if it would help. Bruce Therion 5.2.10 ######################## pdftex log file ######################### This is pdfTeX, Version 3.1415926-1.40.10 (Web2C 7.5.7) (format=pdftex 2009.5.24) 29 JUN 2011 14:48 entering extended mode **data.tex (./data.tex (./th_enc.tex) (./th_texts.tex) (./th_resources.tex (c:/Program Files/Therion/texmf/tex/glyphtounicode.tex)) (./th_fontdef.tex{c:/P rogram Files/Therion/texmf/fonts/pdftex.map}) (./th_formdef.tex Normal \count register pool exhausted, switching to extended pool.) (./th_pagedef.tex <./pic0003.png> <./pic0006.png>) (./th_pages.tex) 253 numeric registers used out of 32768 [1] ) Therion 5.3 ######################## pdftex log file ######################### This is pdfTeX, Version 3.1415926-1.40.10 (Web2C 2009) (format=pdftex 2010.1.2) 29 JUN 2011 14:55 entering extended mode **data.tex (./data.tex (./th_enc.tex) (./th_texts.tex) (./th_resources.tex (c:/Program Files/Therion/texmf/tex/glyphtounicode.tex)) (./th_fontdef.tex{c:/P rogram Files/Therion/texmf/fonts/pdftex.map}) (./th_formdef.tex Normal \count register pool exhausted, switching to extended pool.) (./th_pagedef.tex <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.pn g> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.p ng> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006. png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003 .png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic000 6.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic00 03.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0 006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic 0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pi c0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./p ic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./ pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <. /pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> < ./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png> <./pic0003.png> <./pic0006.png >) (./th_pages.tex) 253 numeric registers used out of 32768 [1] )