I'd start with changing a few of your PDF export settings to see if that helps. First you mention that you're making PDF X1a out of Quark 8.5. An X1a is going to be pre-flattened.
In my experience Quark does a terrible job of transparency flattening. Try making a PDF with the same settings but turn change the export settings to Export transparency natively. If the Quark transparency flattener is causing the issue, the resulting PDF should be good. If your workflow requires a flattened file you can use the transparency flattener in Acrobat to flatten the file before processing. I've seen much better results using the Adobe flattener.
The second thing to try is to export an unflattened ps out of Quark and then try converting it with Distiller. Just change your Quark prefs to "convert to postscript file for later distilling" in the PDF section. (It probably couldn't hurt to up the Virtual Memory a little in this window as well). Then take the resulting .ps file and run that through Distiller. The built in Quark PDF export sometimes get's a little flaky with certain files. Switching to Distiller can help.
If you want to keep the transparency live this thread has some info on how to edit your Distiller settings to honor live transparency in Quark .ps files.
http://printplanet.com/forums/quark/20355-quark-8-1-native-transparency-pdf-export
Shawn