You did tune it correctly right? The game requires it be in tune, or you will miss notes even if you are playing correctly. You also need mute OFF, as this game detects your playback just like an amp would. Mute would really screw the game up. This is the main reason why RB3 pro falls short. Not feeling vibration on your fingers makes it feel fake. Turning that off and your multiplier breaks constantly.
In short, Rock Band 3 pro mode falls short.. this game is far better. I still love Pro drums, and standard guitar.. but I wont be buying pro songs in rock band 3 anymore. About $150 in pro songs now that I won't touch again.