Thats not good   Is it an early revision as the site suggests that they can be easily removed. Have you swapped pin assignments in Mach for X and A to see if the A works and X doesnt? If its still A not  working then it would suggest that its a drive or mobo issue and probably best to contact Gecko to see what they suggest.
Hood

My gecko does not have the option to move the drivers, they are static on a motherboard that attatches to the main board. 

I think you're mistaken. They should just plug in. The website even says "Easy to service, removable drives"

ok, let me pop that sucker open and give it the once over...

Ok, I see how this thing works now, the drivers are seperate on the botom main board.  I have switched out A for X and X still works, and A does not...Same symptoms with thedriver boards swapped.  It has to be a software config problem.

I think you have a cable problem.... you said the charge pump was switched off to get it to come out of fault but looking at the xml I think the charge pump should work properly... the charge pump on in e stop was checked and the pins looked correct.
Check the cable for continuity on all the pins.
I dislike the female connector on the g540 simply because a male to female cable will usually be a straight through / extension cable, but a male to male cable is more likely to be a serial or crossover or custom configuration...
but I think thats the only thing about them I don't like , I have several male to male adapters from days gone by 

As Pandinus says it could well be the cable, you know the motors are good,  you know the drives are good so that leaves Mach, the parallel port, the cable or the G540 mobo as the culprits.
 If you swap pins for X and A  in Ports and Pins and the X motor still works then you know its a config issue, if the problem swaps then its hardware.

Hood

Hey Crash,
  When you jog "X", does your "A(4)" DRO show movement as well ? Assume you did the restart after the slave setting.

Anybody....I"ve tried all I can find and cannot simulate A slaved to X .
Is the A dro disabled when slaved ? The manual suggests removing the slaved dro due to it not displaying offsets correctly to avoid confusion.
Un-slaved, it jogs and simulates as it should, slave it and restart then no dro movement for a.
I farted with this for quite a while last night and gave up.
I must be overlooking something. Tried ver 04, 20, 29 and 33.
Russ

The DRO on the main screen shows up, I do not know how to remove it.

Crash, the dro shows up here too as it should.
I'm asking you if your A dro displays the same positions as the x dro when you are jogging x.
On mine, the A dro never changes, always 0.0000
Russ

no, it stays at 0.00000