I don't know if the team's heard this one before, but I figured it'd be worth posting here anyway.
There's a pretty obvious big with Those!, which I'm quite sure exists in vanilla FO3 as well, to do with the Staging of the quest. Basically, what happens is that if you find Wilks' dead father before talking to Wilks, then the objective to find Wilks' father remains open indefinitely, regardless of player action.
Now, I'm pretty sure that it doesn't stop the quest from closing. Reasonably sure. I'll need to finish the quest another time to check that - this is the third time I've encountered it, but I haven't played TTW for ages and I can't remember if the quest stayed open or not, or if I setstaged through, or what. It's by no means game-breaking, but it should probably get fixed at some stage.
Anyway, just thought you guys should know! I'm about 99% sure it ain't a mod conflict. Should exist in vanilla, too. I'm willing to test it a little more if you feel it needs more experimentation.
Hope this helped!
- MarchUntoTorment
P.S. I had no idea where to post this, so feel free to move it if you had to!