I've been going through some similar problems. Lately (past year-ish) I've been gaining weight, but had diarrhea most of the time. I've asked my Dr.'s about it, and they seem to think that it's my body responding to the lack of nutrition -- i.e. My body is taking everything out of what it can in order to compinsate for the quick "turn-around" of food. The thing that sucks about it is that I have a pretty healthy diet, and the most easily absorbed substance from food is fat, so the body hoards what it can.
That's what I've been told. It sucks though, because I was hoping that I'd at least have a smokin' hot body with all the pain and bathroom runs, right?! Heh. I guess we crohnies can find humor in the smallest things...
Let me know if you have any sort of answers? Thanks, and good luck.