I have two thoughts for your problems. I have not set my machine up yet so no direct experience but remember reading in the plugin doc that there is a command buffer rate or amount that one can adjust. If its large, there may be a delay during the homing that lets it get by the switch, or the acceleration is low and it does not decelerate fast enough to stop withing the switch hysteresis.
I don't think the work coordinate system issue is in the Galil card, they can be hard to manage in the cnc control. I've only set the g54 g55 etc on the offsets screen, but move to locations withing a work system with gcode.
Hope this helps,
Mark