It sounds very odd how it could be a problem on the controllers end when it works fine on HOS as explained earlier.
I'd be greatful if people tested any USB controller at all just to make sure.
I have tested on both the official Switch dock and a third-party one and all results end up the same,
Works on HOS (OFW) but not on Atmosphere.
Kinda hard, unless there is someone with the same controller, and same firmware and Atmosphere build, like @impeeza said you might have to use to use Mission Control.












