Thanks Grahm, that was the problem, as I did not realize that you needed to do this when using the charge pump. I have now done this and it works, but I still have a problem.
If I exit Mach 3 the charge pump works as expected and disables the output, however if I then go back into Mach 3, rather than the Output Status light coming on, it just flickers and the motor "twitch" and wont jog properly. If I re-boot the computer, it works properly again but only for the first time I run Mach 3, after that I am back to the flicker.
Does anyone have any ideas as to what is happening?
Thanks