Your description is using the terms Reader and Acrobat interchangeably, though they're not the same. If you are in fact running Acrobat when getting the file-corrupt popup warning, use Acrobat's Pre-flight PDF Syntax analyzer (Tools -> Print Production -> Preflight -> PDF analysis -> Report PDF syntax issues) to see if it will give you further details.
Other PDF viewing utilities may choose to ignore the problem and not tell you about it, especially if it will not affect rendering for viewing, but Acrobat (and perhaps Reader as well) are pickier about flagging problems detected when parsing the input document.
Finally, if you're in an Acrobat session that's given you the complaint about the document, try doing a SaveAs to another PDF filename, then see if that new output file will generate the same complaints when opened in a fresh session. Acrobat may do certain repairs on the fly, depending on the nature of the problem with the input.