Your xml looks fine, obviously you have disabled most things but apart from that I see no problems.
Can you disconnect the parallel port cable from the computer and see if you can reset.
Hood

Yes I can reset after I pull the cable and when I turn the controller off

Ok so that proves Mach and Vista are fine as far as the Reset issue is concerned.
What I would do next is pull all the DB9 plugs, pull all the wiring out of the terminal strip on the G540 with the exception of the power supply (pins 11 and 12) and plug back in the Port cable and power up your supply.
See if Mach is OK still, if not would seem its a G540 problem. In the mean time I will have a look on Geckos site and see if there is info on it there as I am not familiar with them.
Hood

Ok having a look through the manual you will also need a jumper wire between pin 10 and 12 or the G540 will fault (this is because you dont have your E-Stop wired in at the moment)

Hood

Ok its worth looking at the G540 manual as there is a lot more info, look at page 1 for initial setup especially the charge pump disable switch.
http://geckodrive.com/upload/G540%20REV4%20MANUAL.pdf
Hood

Ok so I disconnected all the wires to the g540 except for pins 10, 11, and 12

10 goes to estop c
11 goes to 48+ on psu
12 goes to ground on psu
Ground on psu connects to nc on estop

Still the same problem

I then totally disconnected the estop

10 jumps to 12 then connects to ground on psu
11 connects to 48+ on psu

still the same problem

One other thing, if you have an ohm meter check the parallel cable is direct through pin for pin.
Hood

Thanks hood, running in town to pick one up I guess I should have one.

I also placed a overnight order for a new parallel port card and cable just in case.

Hopefully this will work.

Thanks again for all your help and I will keep you updated.

Did  you do the test, mentioned at  the bottom of page one in the G540 manual, to get the green LED?
Hood

Yes I did the test with the charge pump.

When disabled it turns to green,

When wired to the estop that I had it was green and when pressed it switched to fault or turned red. Plus I tried with one of the motors pluged in and it is pproviding a charge to the motor as well as you cannot turn it. So I don't think it is a problem with the g540 but with either the cable as you mentioned or a problem with the parallel card. At least I hope.