John,
It sounds like something is wrong in the configuration! The best advice I can give is to have ONLY one axis configured to work and test it. IF it works correctly, then disable that axis and move on to the next one. Repeat as necessary.
Back when I was setting mine up, I found that if one axis was not exactly correct, then all will fail as you have noted. Also, when checking out an axis, I would trip it in the middle of the return by hand. That way, I could make a change as necessary without having to go through the jog screen etc to back it off the limit. To check each switch before trying, I use the "Active Port" feature "F2" "<ALT>+F2" and then manually move the switches to confirm proper action.
Then to further confuse the issue, I have modified Turbocnc to allow single axis homing in MDI. Then I have an aux. Z axis homing switch and under g-code, home to it with a tool in the quill and it will automatically handle tool length compensation:})
Bubba