Have you had any issues with the latest nightlies for Wii U?
I resynced my wiiu pro controller, and both (official) wiimotes. This time, I synced my controllers in this order.
1: wiiu pro
2: wiimote plain
3: wiimote with motion plus built inside
I loaded retroarch, and my previously created user 3 bindings were working with the plain wiimote. But when I went to set user 4 bindings with my wiimotion plus controller, it didn't work.
Sooo, I'm guessing a retroarch issue??