What version of InDesign?
What Operating System?
What PDF settings are you using?
Operating system: 10.6.8
I think we've seen similar repots before. First, make sure ID is patched to 7.5.3. My recollection is that either overriding the offending objects onto the document page, or grouping with something else, will alleviate the problem.
Persoanlly, I'd try grouping, using an empty frame, if necessary, on the pasteboard.