Try the following steps if your whammy bar isn't working:
-First, calibrate the whammy bar by going to the "Options" at the main menu, then to "Guitar" and to "Calibrate Whammy". Use your whammy bar a couple times. If the drawing does not show a complete skeleton of the man pointing down at the woman, leave your whammy bar at its resting place (when not in use) then press Green. Use your whammy bar again. If it shows a complete picture, you are done. If it does not show a complete picture, proceed with the next method.
-If the above resolution does not work, go to the "Home" menu, then to "Wii Remote Settings", and finally to "Reconnect". Press 1 + 2. Do not touch the whammy bar while doing this/ Your Wiimote should be reconnected and your whammy bar should work.