>>5
Word on the street is that Trevorchan has questionable security. I don't know its status now but that was what I heard last. It has a good featureset, though.

I don't understand your problem with Wakaba, it almost sounds like you didn't have each instance of it in a different directory. I still don't know why Wakaba never had a simple way to have multiple boards. I know some sites have hacked it or put a convenient frontend on top of it so that this is simplified.