AlanJay, what's your MySQL version? I remember dealing with a bug in MySQL 4.0.x when "find threads started by user" query didn't use the proper indexes. Repairing the thread and post tables fixed that, but after some time the problem crept back in.
Update: found the same bug in the bookmarks, it appears not only 4.0.x are affected:
http://www.vbulletin.com/forum/bugs....iew&bugid=4159
Looks like an intermittent index loss or corruption.
Also, FYI sphinx-0.9.7-rc1 has been released.
Another update: forgot to say that the crash bug has been fixed in RC1.