I just spent a full day trying to figure out what was causing my sessions to get corrupted and the general system instability. I believe it is a combination of a hard drive error and outdated plugins.
Everyone follow along at home:
Check all your drives for errors.
Install the latest version of Pro Tools, 7.4 cs4.
Run the digidesign plugin updater. http://www.digidesign.com/index.cfm?langid=100&navid=54&itemid=28250
Check all your other plugins to verify they are up to date.