Ah yes I see what you mean now.
One method is to have a Flattening Preset set really low
So in Edit>Transparency Flattener, select Low and choose New (this bases a new preset on Low)
Call it Really Low or something.
for the Raster/Vector Balance type in “1”
Line art and text resolution: 72 ppi
Gradient Mesh Resolution: 60 ppi
Tick Convert All Text to Outlines (not sure if this is necessary, but didn't do me any harm)
Then Export you PDF
Choose Acrobat 4 (PDF 1.3)
Go to Output
And change the Transparency flattener to the one you created.
Export the PDF and you should get a really visual PDF that shows where the interaction of the transparency is
I have uploaded PDF sample here
https://www.yousendit.com/trans…..MUJFQlE9PQ
You can clearly see where the interaction occurs.
Now you can go back to your PDF and make it better.
Another test file for you to download (all I did was bring the text to the front)
https://www.yousendit.com/trans…..a1UwTVE9PQ
And then you have that fixed.
Once you've fixed everything you can go back to your regularly scheduled PDF output settings.