I'm not sure what caused it, exactly, but I have a suspicion that it might be exporting maps. After I exported/imported a map, to copy it, I went back to the original map and every screen that had tiles on it had, what looked like, random combos thrown on it. Most of them were combo 0, too
I'm pretty sure it's from exporting the map, because the maps used as layers weren't affected
[Edit] Bit of an interesting discovery. As I was going back and fixing the map, I noticed that some of the screens looked a bit familiar. Turns out that ZQuest sort of shifted the screens, or the combos at least. They were moved two screens to the left, and a half-screen down
Don't know if that's relevant or not, but I though I'd share it just in case