@dc42 I consulted with the odrive developers, and they said that the step pulse interval was 2 microseconds, and all other values could be zero, So my values now are T0:2:0:0 I tested this witha couple of test prints, and it seems to be working good now.

@kooper swap the cables between the boards to rule out its an issue with those maybe.

@dc42 Great thanks! Are there any resources about implementing something like this?

@dc42 that would be awsome, I am guessing that the encoder will be used primarily for position/movement verification.
I have a stepper driver that supports the use of an encoder for position verification and commutating the stepper motor as high pole count bldc to run a control loop on the curent of being applied to maintain rotor position. It can help quite the stepper down versus the standard noisier position verification mode but I don't think there is much to be gained over the existing silent nature of the trinamic drivers using that approach. One advantage it does provide is the ability to momentarily over drive the motor to overcome a high torque demand that would normally cause a stepped to miss a step.

All in all really exciting news