Thanks! My mother had the same issue with Safari 5.1.7.
The PDFs were handled by the QuickTime plugin, instead of the internal PDF renderer.
After deleting the mentioned QuickTime plugin preference files, PDFs are again handled by Safari internally, and QuickTime on the otherside takes care of movie contents.
Things again as they should be.
The following solved by PDF viewing problem.
The fix is in the Adobe program.
Open Adobe program...not viewing files..just start up the program..
CLICK on EDIT at top of page,
....At BOTTOM of page UNCHECK "Enable Protected Mode at startup"
Problem solved. Files will now download and open for use.