If you want to "square the gantry" don't check "Home Slave with Master Axis"
Are you using the LPT? If using another device then it must be approached differently.
I do not use "refcombination" and I am not sure it works to square the gantry anyway.
You want to home the Y before the A.
Use this in the macro,
DoOEMButton (1024) 'ref Z
DoOEMButton (1022) 'ref X
DoOEMButton (1023) 'ref Y
DoOEMButton (1025) 'ref A
This is what should happen,
Z will home, followed by X then when Y goes, A will follow along in sync and after that A will do it while Y stays still.
If using a smoothstepper let me know and I will revise the above.
Greg