I assume that you can jog so movement is working? The first thing is to check there is homing code behind each button. Which button are you clicking? On my "reference" copy of M3 (on laptop not connected to machine) this is the code behind "REF ALL HOME" on the run screen:

DoButton( 24 )
DoButton( 23 )
DoButton( 22 )
DoButton( 25 )

DoOEMButton(133)
DoOEMButton(134)
DoOEMButton(135)

I think those buttons are not linked to any code that causes the machine to move they just zero DROs. To see the code select "edit button script" from the operator menu - buttons with linked scripts will flash - click the one you want to look at.