Do you have a home switch installed for each motor on the Y axis? If not, and you are only using 1 switch, then check off "Home Slave with Master Axis" in General Config as Jeff pointed out. If you have a switch for each motor, though, you should leave that unchecked and instead redo the vbscript behind your Ref All Home button to use the proper RefCombination() in place of the current command that only references Y...
I hope that helps,
scott