Re: bb_meta corrupted?
If only that one table is open when MySQL crashes, you might have exactly this problem. Posts, users and topics are all stored in other tables, but the theme and plugins you’re using are indeed recorded in bb_topicmeta (in my 0.9.0.4 installation). So, if bb_topicmeta gets corrupted, I could see this happening. The database version is stored there as well, and if bbPress doesn’t find that, I think you would get the “upgrade the database” message as well.
I think the question is to find out why MySQL or the server is crashing.