Holy wow, that actually worked, for both my levels (a new one and a really, really old one)! I just copied (and still leaving) the folders from the mod folder to the editor folder and it worked. Maybe it won't solve everyone's problem, and we'll whether that creates any problems, but it's a great start if not all you have to do to solve this. Yet, you still had terrains not work, so maybe not a fix-all, but it fixed all for me at least (for now).
Trust me, I've stuck through this for a while now. I almost gave up on Of Doves and Demons because of the silliest thing (triggers named with dashes in them causing the code to break), but with Rat on the team, we're making great progress and, like you say, the mod has far exceeded my expectations. And Jekyl, we've got many, many past versions stockpiling up on dropbox now. Version control is essential to making a big mod, or else some mistake or bug may ruin everything.
Glad to hear someone else is working on a mod, and that Larian should be supporting us better fairly soon. And thanks for the tip, has upped my motivation to know it's not an insurmountable bug.