Try one of these steps which I normally give out to people who have issues with GamePad for some games:
#1 didn't work for you so try #2
Classic Controller Resync #1:
In game Classic Controller must be resynced by pressing the Home button on the GamePad and then pressing the Home button again to exit back into the game.
Classic Controller Resync #2:
- Press the HOME button on GamePad to get to the Home Menu.
- Hold POWER button on GamePad until the GamePad turns off, this will only turn off the GamePad not the WiiU console.
- Wait a few seconds, then press the POWER button on the GamePad to turn it back on.
- Press any button on the GamePad a few times to re sync.
- If successful, you will see the hand/finger pointer on the screen which you can move with the left analogue stick.
- Press the HOME button on the GamePad to return to the game.
- GamePad should now emulate the Classic Controller.