Hi,
dont know what the fault it but I don't think it is a charge pump fault. Does you breakout board require a charge pump? This was the original idea
behind the charge pump, if Mach was active and working it would produce a charge pump signal, in absence of the signal the board would shutdown.
Not many people use it anymore.
In the manual there is a procedure for testing the encoder, did you follow it? The only other thing that occurs to me is that you have the motor going backwards,
the step/dir signal say go 2000 pulses clockwise but the motor takes off in the wrong direction. Easy to swap the two motor wires an try it.
Craig