Does your setup think the homing switch is a limit switch? Try setting soft limits correctly and turning them on.
No and soft limits are on and set correctly. I have separate limit switches and homing switches.
The homing switches are a bit in from the limit switches at the homing side of the axis. The Z homing is real far from the limit switch because it has to move above homing to do the tool change. It should never hit the limit switches, but if you did hit the limit switches by doing something wrong your dead in the water because they kill everything until you hold down my limit override switch to bring it off of them. It should never hit the actual limit switches during normal operation unless something is done wrong.
When it says this stuff on boot up, no switch is active. From what they said on the Warp9 forum this could just be that it sees something active during the boot up sequence before it is all done initializing, but is not really a problem since it is not really an issue once it is all booted up and homed.
From the Warp9 forum:
"......Depending on your wiring, your specific limit switches and your break out board, your limit switch signal may very well be active (as supplied to the ESS input pin) even though your limit switch itself may not be activated. A lot depends on the power up sequence and states of that other hardware. That being said, there is no issue with just ignoring that message at startup,and as soon as you press the enable button that message will be gone (assuming you are using v246 of the ESS plugin)."