X direction not changing consistently

Your joints are missing these setting (don't use mine as they are too short, use 5000)

# these are in nanoseconds
DIRSETUP   = 500
DIRHOLD    = 500
STEPLEN    = 1000
STEPSPACE  = 1000
STEP_SCALE = 1000

oldtech wrote:

I recently had the same issue. This may not be your solution, but I recommend that you double check your wiring, and in particular all connections, to your driver and from your driver to your stepper. In my case, I discovered that I was using bad connectors along with not being careful enough when using the screw connectors even though I had carefully checked for continuity and signal on all the lines. Being more careful with the screw connectors and replacing the connectors with Molex connectors fixed it.

Another possibility is EMI. Are you using shielded lines properly terminated?

Exactly the same thing happened here last weekend. Took me a while to figure out but it was a bad connector on the z-axis. Seems to happen a lot.
 

Days later, and after changing both the stepper motor and the BOB, I tracked down the culprit. The wire carrying the +5V to the stepper driver had a hidden intermittent fracture inside it. Because it was intermittent, and because I was measuring the voltage on the step/dir terminals wrt 0V, it took me 10 days to discover it.