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We had similar issues and found the culprit was McAfee holding things open too long and Domino timing out trying to get to them or even another attempt to access the same thing came round (and caused a Server crash).
Upgraded and fully Patched McAfee is now behaving.
Check which files have Transaction Logging (don't need it on Mail.box for example)
Schedule_disabletxnlogging=1
MailBoxDisableTXNLogging=1
LOG_DisableTXNLogging=1
Check your AV exclusions too.
Hope this helps in some way.
Ian
Feedback response number WEBB96LL2E created by ~John Chufreeteroni on 04/09/2013