Once you initialize the two axis in the gearing mode, which I assume you are using to slave the D, they should track together, if you try and have a home sequence for both and they are bolted rigidly then there is going to be stress on one side if the home position for both is different occurs at a different position, the alternative is to have a swivel joint on one side and they will orient square when homed if the switches are set up right.
Another way if the gantry is rigid is to have a home switch on the X only.
A method that MG Systems used once on their gantry's was to have a swivel joint on one side, they would drive both axis to one end of the table where two rubber/pneumatic bumper's where set, the torque limit in the controller was set down low enough that when the cushions bottomed out the position error limit was detected in the controller and the gantry was declared square, the Gearing command was given at this point to lock the axis and the X search for the marker pulse for home.
Rather elaborate, but it seemed to work pretty good.
I have not used Galil with Mach as yet.
Not sure about the limit problems, depends on what make and how wired?
Al.
CNC, Mechatronics Integration and Custom Machine Design
“Logic will get you from A to B. Imagination will take you everywhere.”
Albert E.