How to flatten ID pdf?

I've had trouble with my .pdf files not being flattened to one layer after exporting from ID CS4. I have to open them in PS and hit flatten image or I get shadows around some of the text. How can I flatten the layers before exporting?  Thanks!

Ok Ed. It's best if you post the pdf somewhere for someone to look at to best direct you.
It's clear you don't know some of the terms that are used, which is fine.
The information you have given us is not near enough to give real feedback on the problem.
From the reason that the printer gave you (or the reason that you posted that the printer couldn't use the pdf) seems to me that the printer didn't really know how to fix the problem either.
Not having a go at you or your printer. But if you can't tell us what compatibility level you used in making the pdf or what "set to overprint" means it would be very hard to instruct you further.
That's why we need to see the PDF to work out what is going on.
That way we can help you understand it better. At the moment, you can't answer the questions we need answered to help you. So it's best if someone examines the PDF and then give you tips on how to avoid this in the future.

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