I think that we nailed a problem of script time out sometimes, it look like it is related to email routine if in thread exist people who are subscribed to receive messages or if a private message is send (most people have option to get notification on private messages), problem exist in our board so much as we converted a old board to new one and in conversion process install routine add to all old users activation both email notification for threads and private messages, as many people never looked at profile and changed it this mean 80%+ of 17.000 our users have by default option to get notification of all posts.
Probably a email routine get overloaded in some situation and is creating a problems and timeout of script that in consequence never finish and never update number of replies, last posted, user posts and other things.
It will be big help to fix UPGRADE script so that it don't set email notification by default and also to check if anything can be done to email routine to not stack too much emails all at once as this look to be main problem, this can depend probably only in some combinations of mail program software "sendmail ??" and Php version ?? I'm not sure but I hope this at last give idea where to look about this problem !!