This seems alot like an old bug with the installer. Did you have alot of PMs? One of the altertables (maybe 6.2) used to time out and essentially lose all the user ids for the private messages.
http://www.ubbcentral.com/boards/showflat.php?Cat=0&Board=UBB8&Number=21374Basically all PMs got reset to user #1 (which will appear as deleted user)
Although you were already on 6.2.... so you should have been past that hurdle.
Is it possible that you accidentally ran the 6.1-6.2 altertable. None of the altertables from 6.2 through 6.5 do anything at all to the Private Messages table. So there must be something else amis.
At this point, if all PMs have been assigned to user#1, then there's not much you can do about it, other than restore a backup of the w3t_Messages table. Searching through the altertables, I don't believe there were any changes to the w3t_Messages table, so plunking the old table back in there should be fine.