Sorry to take so long to respond to your last question, but I've been pouring over the settings to see if I could find a quick answer for you. Not finding anything that stands out. But a couple of questions for you:
1. Is your Z Axis set to home in a positive direction (i.e. Zero at the top of the movement)?
2. Does your Z Axis move UP for positive values and DOWN for negative?
It's possible the logic in your configurations is reversed at one setting or another. So when it homes, it could be possible that it's moving to the limit and then trying to move further in the same direction to "back off" the home/limit switch. You'd probably know this, however, as you'd be hearing it try to continue as it crashes into the mechanical limit of the machine. But it's something to check. Make sure the Z Axis moves up for positive and down for negative and then check that "Home Negative" is UNCHECKED so that it knows it is the positive limit it is looking for. Then when it tries to home the axis, it should seek the upper limit switch and then back off until the switch is no longer active.
This, of course, assumes you are using shared home/limit switches. The same should be true if you have a dedicated home switch as well but I do not know for sure.
Stephen "Highspeed" Kruse