I tested pdf passthrough with simple pdfs. One thing is interesting: when I place a document in a Publisher file it is passed through, when I put directly from the finder it is not passed through. The fonts are wrongly replaced.
When I change to interprete:
I cannot interpret both pdfs, the right looses the right font, but also cannot be interpreted.
Creating PDFs
When I directly export as PDF all is ok, both pdfs are right
when at first I make a PostscriptFile and then distill it to pdf it is not right.
And one suggestion: Could you please make possible to export as Postscript. Sometimes it is a good job to distill via Distiller. The standard printing dialog is not that ok.