Nintendo Switch Pro Controller Issues.

Greetings.

I'm getting the weirdest issue here. I hope someone can help me:

I'm using the Pro Controller. When I open the game, controller doesn't work properly in the menu. It seems to work as a keyboard and mouse. I can control the mouse through the joysticks, RT is left click, etc. And is not changing when I get into game mode. In the menu, buttons should change from Q and E to LT and RT to change between Equip, Preferences, etc.

BUT

Accidentally, I got into Campaign Mode, and in that mode, Controller works perfectly! No Issues in the menu, neither in the gameplay. 

Does anybody have an idea? Thanks in advance.