Post that over on the CNCzone's Gecko forum, http://www.cnczone.com/forums/forumdisplay.php?f=31 , and I bet you get an answer from Mariss, or a gecko user, within an hour.
I'd like to help, but I've only wired one G540, and it, and the documentation, is over at my parents' .
Jack I had a similar problem on initial setup. Had to "Fix" the bios setting on the computer I think if you read the below link you will find the answer. I was scratching my head on this one too except I do not recall a charge pump switch on my gecko you may have a later release.
G540InitialSetup.pdf
This should help.
Also make sure you have your e-stop wired for Normally closed (NC) mode and you have the e-stop set for active low in the software. I am also guilty of wiring the e-stop on the wrong side of the switch (NO) this would work but not best practice. Where is that little smiley under the chair when you need him LOL.