You can turn it off normally by setting it to port 0 pin 0 but you cant physically disable the E-Stop. You can also have pins asigned and just have the active state set the right way and that will do the same.
You obviously have something wrong that you are not able to do that, if you attach your xml I will have a look and see if its any of your settings, if not then maybe a reinstal of Mach would sort it.
Hood