Thanks for the reply.
I did figure the problem out though thanks to this forum.
It turns out that the setup instructions provided with the usbmach board tells you to not assign pins to the mpg and thats the whole problem if you are not using an mpg thats goes thru usb.
What I did was assign pin 10 port 1 to estop, and the mpg i assigned pin 12,13,14 and 15 on port 1 and low and behold it works as intended.