I've had my WM+ cut out a few times while playing GST. Once I unplugged the nunchuck and plugged it back it, it would respond. Once I had the entire controller shut down and would not fire back up unless I unplugged the WM+ and then it worked again.
Its only happened to me during GST so it might be the game. If your having troubles with the nunchuck working while the WM+ is connected, try restarting the game, changing the batteries, reconnecting the WM+ or try a different nunchuck + wiimote combo. If none of that works, you might have a defective unit and I would return it or call up Nintendo