I've had this problem two or three times where my diff and merge preferences get clobbered (reset from FileMerge to blank). Thankfully I find this post which reminds me to re-add them. On at least the last two times that this happened, the problem occurred after restarting my machine, which I only do rarely.
I'd argue that this is a usability bug, albeit a minor one. MacHg should detect the situation and do something a bit more sensible.