Apply standard troubleshooting practice.
You have 1 working axis and 2 not working axes. All otherwise identical in pitch/steps, right?
Swap things around... amps, motors, wiring, etc. Keep close track of what you do and where things move and where the problem goes. Use process of elimination to isolate the cause.
My guess... wiring issue that's introducing/mangling pulses w/r/t ground or some such. Common with stepper amp wiring.
Good luck!