If you want to know more about the history of a "flaky" InDesign file, here's something to try. Hold down command (Mac) or ctrl (Windows) as you select About InDesign from the InDesign menu (Mac) or the Help menu (Windows). This will display the "Component Information" dialog box. Among other things, this will show you the complete history of every "Save As" in the life of the document, whether it has ever crossed platform from Windows to Mac or vice versa, and if the document was ever converted from QuarkXPress or PageMaker.
InDesign can convert Quark 4 files to InDesign format, and newer Quark files can be converted with the Q2ID plug-in. Here's the problem: the Component Information dialog box will only state that a file was converted from Quark if it was converted using InDesign's native Quark 4 conversion. If the file was converted to Quark using the Q2ID plug-in, the dialog box will display "Converted from QuarkXPress - no". So beware of this. I don't know of any way to tell after the fact whether a file has been converted to InDesign format using the Q2ID plug-in.