Here's another update on my troubled file with this issue...
The file is a rather simple 2-color, 1 page document containing text, a couple of placed graphics (including a bitmap Photoshop image), and some boxes of color. One of the graphics has a drop shadow applied to it. The drop shadow sits over the Photoshop bitmap image which has been colored by Quark (fake monotone). Then the designer has applied different values of the color to the foreground and background.
Trying different flattener resolutions, using the "As Is" color output option, and updating Quark to 7.31 didn't help. If I remove the drop shadow, I get a PDF. If I remove the bitmap image, I get a PDF. If I remove both, I get a PDF.
To get around this, I removed the drop shadow and saved the Q7 file to Q4 and opened it with InDesign CS2. After re-applying the drop shadow with InDesign, I was able get a good PDF of the file.