I have exactly that same issue. I see that there's a related topic, but my non-existent French prevents me from understanding anything.

version: 4.1 unstable
system RPi3
I can use the Classic controller on the menus, but the moment I enter the game, I can't use it anymore. The Wiimote can be used, but the axis is reversed (to be used vertically instead of horizontally).

Thanks for your time!

PD: Edited for typos