Hey Stuart,
Depending on the motion controller the Reverse Checkbox will change it.
I've had to do just as you, change the high to low in the Plugin Config for an ESS here at work, but on the HiCON Integra, I just have to check this checkbox I am referring to.
Personally, I think the Mach Configure Checkbox should be the Reverse Override and not the plugin pin output, it should communicate that information over to the motion controller.