I've gone through the entire original campaign without any issues but now I've progressed into SoD I seem to be getting a constant lowering of my reputation. It seems to be a caused by one of my mods.
I only started noticing it when companions began to complain shortly after recruiting them, I thought it perhaps a minor issue and used Keeper to bump it back up. However, it keeps happening.
I seem to take a hit to my rep every time I kill something (only tested it with killing undead so far). It's almost certainly caused by a mod. I can replicate the bug with a new character, and can eliminate the issuet by deleting my Override folder.
Does anyone know which file or files might be responsible for keeping track of rep relating to what you kill? As a test, I tired just deleting anything with "rep" in the name, but that didn't seem to resolve the issue.