Well, I can't comment on what was causing the problem, but the two overrides I forgot to remove when initially de-modding my game were Highlight Everything (which has never actually seemed to work for me, incidentally), and Mod Fixer.
It has to do with ModFixer according to the discussions in that mods comment section. If ModFixer is just sitting in the modfolder, there is no problem, but as soon as it has to get work, because a mod is added, that requires ModFixer, then the trouble begins.
"We are all stories in the end. Just make it a good one."
