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
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