Scott,
There are settings on the amplifier through a keyboard which tell the amplifier to ignore 12 and 13 and use 14 and 15. The Rutex signal is connected to 14 and ground to 15 for sure. The P.OT and N.OT are not activated as this amplifier was wired without limit switches originally to that is not a problem. One thing I am wondering is if the notPCON feature is messing things up. Are you familiar with this feature? Now, the notPCON is open. I think the next thing to try is to connect that pin to 24v and see what happens. There seems to be some noise in the system possibly.
On a good note, I was able this afternoon to get the motor to move in both directions with Mach3! However, the movement is very coggy and it still does not want to move consistently but in one direction. I will try tomorrow to switch the dir to active high and see if that makes a difference. Lots of trial and error, but mostly error...
I have just been advised that the Rutex should be in an electrically isolated box and some caps across the power in to clean up noise. I hope that will make a difference.