Thanks again for your help.
Yes, the Z-Axis works just fine, with the exception of this homing issue. I am using Stepper motors + Gecko Drives.
I did as you suggested and swapped Pins 1 and 2, effectively swapping the limit switches for Y and Z. The problem did not track the limit switch, but stayed with the Z-Axis. Again it homed just fine (expect that I had to manually trip the switches, since the axis was looking for the wrong switch), but the Z-Axis was skipped.
Any other ideas? Is there another level of homing settings past the 'Motor Home/Soft Limits' page? Somehow the Z-Axis is set to just take its current position instead of looking for a switch?