Preview PDF Table of Contents not showing on some files

I have been having a recurring problem with some PDF files. The Table of Contents will not show up in the Sidebar. When I try to select it I either get only the document title or I cannot get anything to show other than the thumbnails. This is frustrating. The bookmarks will show up in Adobe Reader but not in Preview. I need to easily navigate in Preview since I will be doing annotation & note taking, something that cannot be done in Reader.

Previous revisions on some files will show the TOC but the newest ones won't. Sometimes links from the TOC in the document will work - but they don't show in the Sidebar.

This is really frustrating as when I open the Inspector up on the files there does not appear to be anything different between the different revisions.

Any help would be greatly appreciated!