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Regions missing in Pro Tools session

I run a Pro Tools LE setup on Mac OS X, and just upgraded to the lastest version; I believe it's 6.4. Now, when I reopen a session that was worked on after the upgrade, it gives me this message at startup:

"Some regions were removed from the Timeline or Region List because they referred to files which are too short."

Digidesign says this message can be ignored, but when I go into the session some (not all) vital regions are deleted from the edit area. The .wav files are still in the Audio Files directory, so I haven't really lost any recordings, they just won't show up in the timeline. If anyone could help: 1) How do I get the files back in the right spots in the session file? and 2) How do I keep this from happening again? Thanks in advance!