Go to your Documents\My Games\XCOM 2\XComGame\Config\XComEngine.ini and look for every lines that starts with 'ModClassOverrides=', and remove all of them, these lines are added by mods that requires overriding other base game classes, but the game never removes them once you disable the mods, this can easily cause disabled mods to still affect your gameplay.
Whenever you have some mods not working or fail to disable properly, here are 3 steps that you should do first before bugging others, since the game does not properly disable mods when you disable them, this can cause a lot of conflicts when you swap mods out leading to strange behaviours or even crashes.
