Well about teh only thing left is the anti dive setting. It is the % of Vel drop that mach3 sees where it turns OFF the THC to keep it from diving . IF set to high it will turn itself off and not work.
OR there is a problem with the Smooth stepper obeying commands from the THC controller. For that you need to talk to them. IN you rcase it is the SMooth stepper that is doing the work NOT mach3.
OR possibly that your BOB needs a Charge pump signal to turn it on. (not likely as the machine does move)
What screen set are you using ??
(;- TP