One the plugin config general tab, there is the option to configure the limits and homes active low. These check boxes determine how is CN configured. If yours is checked, uncheck it, or visa verse. You may have to go back to the ports and pins page and undo what you did there.
The deal is that you need the Galil to be satisfied as to the switch arrangement first. This is done with the plugin config. Then you need to get Mach lined up in Ports and Pins.
Steve