I had both Soap Making and Alchemy enabled on a bunch of idlers. Also, I do use Therapist, it came with the package.
It doesn't really matter now, I'm dropping Masterwork. Thanks for the replies anyway.
This was just the last of many frustrations I've had with it. Not to belittle the work and effort that's gone into such a huge mod, but it's just not for me. Personal taste, nothing more. I only really picked it up for a couple of features - bonfires and some misc buildings - but I didn't realise that the world would still be massively altered by features that I specifically disabled. Traders were turning up with turrets and landmines in cages. Goblins had silly names like "poke-yer-throat". That sorta thing.
I think the best thing for me would be to just take the specific buildings I want and add them to vanilla manually. I'll miss Masterwork's ini editor, but it wasn't robust enough in disabling the features I wasn't interested in.