Lots of reports on DUC of past problems like this. You should probably be starting there. e.g.
http://duc.avid.com/showthread.php?t=406849
And unless its something as specific as Command 8 drivers or similar I suspect (always suspect) plugins. You can look for crash files and check what is at the end of each Pro Tools log file (e.g. Pro Tools may be failing to really shut down OK at the very end).