Some suggestions.

1. My best guess is that something is altering the graphics state and not restoring it. Not sure if you are doing any translation, rotation, scaling, etc, but make sure graphics state is not being saved & restored (e.g. using PDF::API2's $gfx->save and $gfx->restore on page graphics).

2. If you're getting postscript error's, it could be useful to see them!

3. I've found that ghostscript gives the best diagnostics. If you haven't already, it's worthwhile to try view your pdf's directly with ghostscript, checking for errors. Also convert to postscript using pdf2ps (or xpdf's pdftops) and also view these with ghostscript.

Good luck!