Just had this same issue - activated this mod Skitso's Oppressive UI, used once, decided to deactivate (really loved the vignetted backgrounds but the other stuff wasn't for me), but UI elements still persisted - notably the soldier stats bars stayed grey/black instead of the vanilla/ce colour of green, plus some other minor things. Then I completely uninstalled/reinstalled the game and UI elements from this mod still persisted even then! Just ran a full C:/ search for "Xenonauts" and purged everything - i think you are right it was stuff still in the C:\Users\%username%\AppData\ folders, found a bunch of scripts in the Roaming folder still persisting after game uninstall
