Strange that you bring this up because....
I almost exclusively publish to PDF from the SSM, and I never have any issues. My page setups are *usually* set to "DWG to PDF.PC3", but on occasion I do publish an older sheet set where the page setup may be set to something else. Still, no issues..
Other people here "PLOT" using "DWG to PDF.PC3" (everyone is mapped to the same PC3/PMP files and plot styles), and frequently have issues with wipeouts, background masking, and similar oddities.
I've always felt that publishing is doing something different that PLOT even though both are using the same PC3/PMP files.