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I've had this problem and I think it is related to Time Machine. When the problem occurs programs lock-up, can't be killed so that they can be relaunched (process running in the Dock but not in Activity Monitor) but I've found that when this happens Time Machine is preparing a backup to the attached FireWire disk. Telling Time Machine to cancel the backup doesn't do anything (gridlock condition, perhaps?) but unplugging the disk causes all "orphaned" processes/applications to quit properly. Needless to say, OS X complains that I unplugged the disk without unmounting it properly but it does appear to resolve the issue.
I am not certain if this is the same situation that you are seeing but if you are using Time Machine then I think that's your problem.
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