QuarkXPress 6.x users, have you noticed that its optional OPI XTension is installed and turned on by default? If you're trying to troubleshoot random, bizarre problems with your PDFs or printouts, this could be the culprit.
The OPI XT is only needed if you're a worker bee in an OPI workflow, the kind where you're using low-res images in your layouts (for speed's sake), while their high-res versions are automatically substituted when you output to print or PDF or do a Collect for Output . A big fat OPI image server and OPI software on your network runs the whole shebang. It's not really that common these days except for large publishers with lots of huge images.
Yet for some reason, QuarkXPress 6.x assumes everyone is working in a OPI workflow. Look at the Extensions Manager (in the Utilities menu); the OPI XT is enabled. Look at the OPI panel in the Print dialog: "OPI Active" is checked on. Look at the OPI panel in the PDF Options dialog (Export -> Layout to PDF -> Options): "OPI Active" is turned on there too.
All the OPI XT does is add comments to the flow of internal code indicating that there's an image that needs to be swapped. But that little bit of code can cause random, inexplicable problems in output if there's no high-res image waiting for its turn in the spotlight.
To turn off the OPI XT, just uncheck it in Utilities -> XTension Manager and restart the program. But I prefer to just remove the OPI XT completely, that way I don't have to keep remembering to check its on/off state in the XTension Manager. Go into the QuarkXPress 6.x program folder on your hard drive and drag OPI.xnt out of the XTensions folder into some other place — I keep mine floating in the QuarkXPress program folder. (Don't put it into XTensions Disabled, that's the same as turning it off in the XTensions Manager.) You may need admin privileges to do this in OS X or XP.
By the way, if you're creating PDFs from Quark layouts with Acrobat Distiller, be sure to turn off "Preserve OPI Comments" in the Advanced panel of your Distiller settings as well.