There should never be 12V on ANY output of the PMDX-126. They should go from close to 0V to close to 5V. How do you have the PMDX-126 J4 wired to the G251? And can we presume it is exactly the same as J3 and J2 to other G251 boards?
Measuring voltages on the STEP pin can be tricky. The step pulses are very narrow, and a DC volt meter will end up averaging the waveform with the resulting apparent DC voltage depending on the step frequency and step pulse width. For homing speeds I would expect it to read close to zero volts. The direction signal should be easier to measure as it is relatively static, i.e. zero volts for one direction and 5V for the other (or close to those values). Likewise the LEDs. The "step" LED may flicker dimly during jog moves, and may or may not have visible flicker during homing. The "dir" LED should be definitely on or off depending on the direction of motion.
When homing doesn't move the X axis, can you jog the X axis? Or make it move for any type of motion other than homing?
Is this Mach3 or Mach4?