What version of Ubuntu is this on? If it's on Intrepid (8.10) or
Jaunty, then there's a major regression in the way gnome-session handles
logouts, which results in (almost) all running programs simply being
killed rather than asked to quit nicely.
This looks like it could be a symptom of that bug.
** Changed in: transmission (Ubuntu)
Status: Confirmed => Incomplete
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Transmission should not verify all data when restarted after forced exit by
logout
https://bugs.launchpad.net/bugs/307684
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