Hi Roqmuzik, it sounds as though you may not be getting enough level into your pedal. Can you try boosting the level and making sure you have no other effects going into your pedal to see if your tracking problems remain. Finally, another problem may be if the guitar and pedal have different pitch references. You can check this by making sure you are in tune with the tuner in the pedal, if you're not, this could be the source of the problems. If, after tuning to the pedal, you want to change the pitch reference of the pedal, you can do so in the system menu under, System->Tuner->Calibrate.
Let us know if this doesn't work for you,
Dan
