I've found an inconsistency when converting pdf to swf using PDF2SWF version 8.1. It seems that transparency is only converted correctly in version 1.3?
I have attached a collection of pages with transparency in versions 1.3-1.7 if you want to test it.
As I recall, it worked with 1.4 and 1.5 in version 7 of PDF2SWF (maybe I'm not remembering this correctly)?