You dont have the E-Stop set up to Mach, or at least not in the  xml you attached. I am presuming then that your E-Stop is solely connected to hardware and Mach does not know that you have pressed it, either that or it in some way hooks in to your limit switches.

Do you have a link to any documentation that came with your machine?

Hood

Hood, this is a manual for the breakout board. 

http://www.machmotion.com/pdf/IO6_Board_PP.pdf

Ok from first glance it seems pin 10 is a dedicated pin for E-Stop  so that will be why you have it connected to the voltage with a link.
Do you have any spare pins on your second port you can connect the X switches to?
Do you have another PCI port that you could install and set up as Port 1 instead of the one you are using?
Hood

All the pins on my second port are open, I tried connecting the X up to each one of them and the same problem persisted.  I'm not sure about the PCI port, the mother board is tucked away inside this unit.  Before I start opening up the hardware and CPU I will give the manufacture a call.  Thanks for all your help.

Yes, Mach Motion will be the ones to talk to if you also bought the computer from them.

Hood

I just wanted to let everyone know that I called Mach Motion and we got the problem resolved in a couple minutes.  I had to put M79 into MDI and it opened a setting screen which I then saved.  I don't really know what that did but I am now able to home the machine.  I highly reccomend Mach Motion, I feel that they have the best hardware setup around and their customer service is top notch.

Glad you got it sorted

Hood