Ok.. Gantry homing is somewhat of an issue for me because I don't have a machine with a gantry. But here goes anyway.
First, in the general config, don't home slave with master. In other words, we want Mach to just home the master axis. The slave axis should move with the master as the Galil has them geared together.
Second, in the Galil plugin, select "perform axis squaring".
What this should do is home the master axis while moving the slave axis along with it. Once the mater is homed, the plugin will home the slave if axis squaring is selected (it should be near the home switch at this point anyway).
So try that out and post the debug file if you continue having problems.
Below is what your debug file should look like.
FL 2147483647,2147483647,2147483647,2147483647 Slots=000 Response=":" <DisableSoftLimits() gState.nAixs = 4>
BL -2147483648,-2147483648,-2147483648,-2147483648 Slots=000 Response=":" <DisableSoftLimits() gState.nAixs = 4>
AC ,250000 Slots=000 Response=":" <HomeAxis(1)>
DC ,67107840 Slots=000 Response=":" <HomeAxis(1)>
JGB=8332 Slots=000 Response=":" <HomeAxis(1)>
BG B Slots=000 Response=":" <HomeAxis(1)>
JGB=0 Slots=000 Response=":" <Update() FINDSWITCH>
ST B Slots=000 Response=":" <Update() FINDSWITCH>
JGB=-833 Slots=000 Response=":" <Update() MOVEOFFSWITCH>
BG B Slots=000 Response=":" <Update() MOVEOFFSWITCH>
JGB=0 Slots=000 Response=":" <Update() ROUGHHOME>
ST B Slots=000 Response=":" <Update() ROUGHHOME>
JGB=0 Slots=000 Response=":" <Update() SYNCSTATE>
ST B Slots=000 Response=":" <Update() SYNCSTATE>
AC ,0 Slots=000 Response=":" <Update() SYNCSTATE>
DC ,0 Slots=000 Response=":" <Update() SYNCSTATE>
DP ,0 Slots=000 Response=":" <Update() SYNCSTATE>
SH B Slots=000 Response=":" <DoHoming() SYNCSTATE>
GM ,,,0 Slots=000 Response=":" <Slave(1, 3, false)> //Uncouple the slave from the master
GR ,,,0 Slots=000 Response=":" <Slave(1, 3, false)> //Uncouple the slave from the master
FL 2147483647,2147483647,2147483647,2147483647 Slots=000 Response=":" <DisableSoftLimits() gState.nAixs = 4>
BL -2147483648,-2147483648,-2147483648,-2147483648 Slots=000 Response=":" <DisableSoftLimits() gState.nAixs = 4>
AC ,,,250000 Slots=000 Response=":" <HomeAxis(3)>
DC ,,,67107840 Slots=000 Response=":" <HomeAxis(3)>
JGD=8332 Slots=000 Response=":" <HomeAxis(3)>
BG D Slots=000 Response=":" <HomeAxis(3)>
JGD=0 Slots=000 Response=":" <Update() FINDSWITCH>
ST D Slots=000 Response=":" <Update() FINDSWITCH>
JGD=-833 Slots=000 Response=":" <Update() MOVEOFFSWITCH>
BG D Slots=000 Response=":" <Update() MOVEOFFSWITCH>
JGD=0 Slots=000 Response=":" <Update() ROUGHHOME>
ST D Slots=000 Response=":" <Update() ROUGHHOME>
JGD=0 Slots=000 Response=":" <Update() SYNCSTATE>
ST D Slots=000 Response=":" <Update() SYNCSTATE>
AC ,,,0 Slots=000 Response=":" <Update() SYNCSTATE>
DC ,,,0 Slots=000 Response=":" <Update() SYNCSTATE>
DP ,,,0 Slots=000 Response=":" <Update() SYNCSTATE>
SH D Slots=000 Response=":" <DoHoming() SYNCSTATE>
CS S Slots=000 Response=":" <DoHoming() NO MORE HOMES>
GA ,,,B Slots=000 Response=":" <Slave(1, 3, true)> // re-couple the slave to the master
GR ,,,1 Slots=000 Response=":" <Slave(1, 3, true)>
GM ,,,1 Slots=000 Response=":" <Slave(1, 3, true)>