It sounds like something is happening in the transaprency flattening, but some screen shots would help of the page in ID and in Acrobat.
Also, what settings are you using during export, and most important of all, waht viewer are you using to look at the PDF?
I was using Apple preview to view the documents. Eventually I tried adobe reader and that solved the problem! Who knew the reader could make a difference - I was looking in the .indd file trying to see what was wrong!