Newline,
Did you solve this one yet? From your post, I'm not entirely sure exactly what is happening. Is it your Y axis that is dual drive? Is the second drive slaved in software (mach) or hardware? If it's slaved in mach then you have to make sure that both axes (primary and slave) are set to home in the correct direction in Homing and Limits. If you are referencing both axes (home switches on both drives) then you have to uncheck the config setting "Home slave with primary" (sorry I may have that config value name wrong but it's something like that). With this unchecked you can home both sides of the gantry and thereby square it every time you reference to home (provided you have two switches on the axis - one for each drive).
Hope this helps!