Incorrect inputs while using Nintendo Switch Pro controller

With this new version of the software (4.17.15.0) I have been having an issue fairly often where my button presses will input to my game as the button matching the controller and not what I have it mapped as in the app. Example: Switch controller has A button where B is on an Xbox controller and vice versa so I have them mapped in the reverse in 360ce for optimal button layout. I have been playing Elden Ring will hit the button to roll (mapped as B on 360ce but is A on controller) but will sometimes jump instead (What "A" does by default in the game without program), causing subsequent death. This also happens with the X and Y buttons, occasionally switching inputs and causing incorrect actions. Any tips to avoid this or is it just a bug I need to play around?