We've been talking with InfoPop about this, and they're telling us that it's a problem with the version that we're using, 5.47. I saw some other, similar complaints on their tech boards involving these problems.
I spoke with one of their programmers, and he actually doesn't recommend we go up to v6 since the amount of traffic we receive would put a big slowdown on the dynamically generated pages version 6 uses. Instead, they suggest UBBThreads or OpenTopic...
We have some other products we're going to look at first, though.
As far as the corrupted threads, though, we can't rebuild them. Once they become munged like they are, they're unrecoverable.