The TRX spur gears are known to be quite finicky even out of the package. Check the 3 screws that tighten the spur to the hub. Id even go as far and trying to reseat the spur gear. Sometimes you can tighten them down to where they get stuck at an angle before seating correctly causing all kinds of off axis running.
Another thing, i dont know if you know this, but if youre using the stock 3500 motor that the motor shaft is extra long so that you mount the pinion backwards. It will have the teeth side of the pinion on first with the grub screw to the outside. See below:
