Sure,
the Version is v3.330 (Wii U)
Built Apr 20 2015 23:10:11
Firmware: 58.25.32
I have the gamecube controller in the slot on the far left when looking at it from the top.
Why don't you use the option inside Nintendont to download the controller ini files. Should work without it but you never know.
Out of curiosity is you Gamecube adapter an Official Nintendo one or a 3rd party. Shouldn't make a difference but you never know.