After you configured it did you select Save Config at teh end of the config menu?
It can be a real pain at times, but if you completely screw up your config and don't select Save config it means that all you have to do is restart Mach3 to get back your machine.
There are a few other places where you have to do something similar, but it is really done that way so you have to deliberately save stuff that will alter your machines behaviour.
Afraid thats not quite true, Mach will (or should) save any changes you make to the xml when you shut Mach down correctly, no need to use Save Config. It is however a good practice to get into and actually in Rev 4 you will not be able to do anything at all in Mach until you have chosen to save after changing config settings.
Hood