OK, here's the deal folks:
After 2 weeks of hard work trying to figure out just what the heck is going on, we've given up. We got the sites back up, but the problems never went away. For instance, we were unable to access the Store, or edit a board, no matter what we did.
We're going back to our 2/21/2010 backup (the first problem was on 2/23/2010). I know it sucks, but if it fixes the problems, it's worth it.
If it gets problematic again, then I'll probably have to kill someone. Just hope it isn't you.
For those of you that need it, we now have a read-only version of the site from the last 2 weeks up:
If you need a post from one of our other sites, let me know. As of right now you can access PM's from any site, but only posts from M3F and FFC.