Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
What happens when you try to just drag them into the trash? Are the files maybe open in Preview or another PDF viewing app?

Try logging out then logging back in then drag to trash.
 
One thing that happens frequently -- if you open the PDF in Preview it stays in use and cannot be deleted even when you close the Preview window. Make sure to quit Preview before trying to trash PDFs.
 
Try this in the exact order:

1. Drag files you don't want to the trash, but DON'T try to empty the trash yet

2. Log out of your account

3. Log BACK INTO your account

4. NOW try to empty the trash.

Any better?
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.