If you try to select an "emulated controller" like Wii u Pro Controller or Wii u Classic Controller,
a bug occurs when you try to save the profile. It is always saved as Wii u GamePad, even if you have specified a different one.

At the moment, in order to workaround, you have to open the controllerprofile folder and manually edit the just saved controller file as follow

emulate = Wii U Pro Controller

once you do this, you have to remap again the buttons as they are miss-mapped.
save again and everything should work.