Brains runs with the update loop of Mach3, currently 10hrtz, in reality the Macro pump runs about 4 - 8 hrtz (even though it should also run with machs update loop). The difference being that the Brains are kinda run like a plugin in a way.
also, brians are a "state" machine type, ie, if you bring in an input that maps to the Estop, and that external estop is pushed, then it will push your Mach3 estop.
but, when the button is released externally, and the input goes back to 0, it does not RePush and take the machine out of estop. You would have to toggle your Estop button to get it to repush. So, in essence the brain looks at changes in single state only. You would have to write other logic in your brain to handle the Estop reseting to stay in synch with your external button, OR, put some Code that always runs in the back ground with your Macropump.
Scott