Just found out that someone here has already emailed you directly on this matter (I didn't know this and he has been out of the office).
I believe he has already sent the GalilDebug.txt file to you.
The "Home slave with master" is indeed NOT checked.
Make sure that the "Home slave with master" is not checked in the Mach General Config.
The Galil plugin puts the master/slave axis in gantry mode. But if Mach sends movement commands to the slave axis, then the movement of the slave axis is doubled!
In the next release, I will handle this case in the code so that no matter how the General Config is setup, it will do the right thing.
But... as Kenny said, a GalilDebug.txt file would be nice to verify this.
Steve