Not sure if this is useful, but I've been able to reproduce the same issue fairly regularly in the following way:

Create and send an SMS to a contact in the normal way, however, before that SMS is actually indicated as being sent (little square arrow thing vanishes) delete the conversation thread entirely.

I'm not really convinced this is the actual trigger of the problem itself rather than just an indicator of the actual cause - which is I think: 'n900 becomes sluggish after a few days'

It happens for me with much greater frequency when my uptime is over the 1 day mark, conversations is often bogged down, takes a while to open incoming messages, the application is slow and the CPU is often pegged at max.

Whatever conversations is doing under the hood, I figure some of it is time sensitive, when the N900 is busy I suspect it doesn't gather all the data points it needs to populate the sqlite db, thus corrupting it.

I guess it would be pretty straight forward to code up a daemon in C to listen for db events and take a look each time a message passes over the bus, though given my suspicion on the cause, it'd also be a good idea to have that daemon wake up every few minutes while the screen is active and do the same check.

I don't have the problem terribly often, so the manual corrections to the sqlite db aren't terribly bothersome.