Ok, I'm about ready to take a hammer to this controller! Per my previous post, I was having trouble with my configuration because my G540 runs in 10x microstepping by default, and cannot be changed. This forced my to use a Z step setting number of 24,000 steps-per-inch (I'm running, or trying to run in inch mode). Max setting is supposed to be not over 10,000. At this setting, my Z-axis just hummed in program running mode, such as when trying to home. When I set this down to a lower number (12,000), it worked perfectly other than being off by 50%. So, I replaced the G540 with some TB6600 motor drivers where I can set microstepping. It was working perfect again on X & Y. I now have Z step setting @ 2400 with the new motor driver (no microstepping), and it's doing the same thing again! Motor won't even move in manual mode unless I drop the Z number to something well below the 2400 I need it to be.
WHAT THE HECK IS GOING ON WITH THIS STUPID THING??

It didn't like 24,000 with the G540, and now it doesn't like 2400 with the TB6600 drivers! There is nothing wrong mechanically with the Z axis, it runs very smooth when I set an artificially low step number.