Well even if the problem is the game just not playing nice with the mods I'm confident you guys will figure it out. The few of you putting mods out already have been doing some cool things in a brand new game engine. I'm impressed.
I'm not sure if this will be good news or bad:
I got a hold of that Tools.lsb and, well, it works together with FoodCombos, for me.
Here were my exact steps:
1) I read your post and Googled for unbreak- well, okay, let's skip ahead a few steps.
2) I'm not using an "empty" master mod in fact, so I did all of my work inside of my own mod's folder, Public \ Fixed_and_Missing_Recipes_85e5adf9-1a66-412d-b24f-71d59331859b.
3) So in that folder, I made a new folder: RootTemplates.
4) I copied Tools.lsb into RootTemplates.
5) Launched my game and tested some of my recipes, then tried picking the door at the end of the hall upstairs in the inn. Recipes worked; I failed to pick and kept my lockpick.
So really, that's all I did. I didn't have to make a new LSB in this case because of my approach... maybe that's a clue. Also just as a sanity check: You do have Stats in a separate *top* level folder, not under RootTemplates, right?
