Ok, I played around with this for a few hours today and nothing seems to change this. It seems like the "Limits Override" button on the settings page has no functionality. Mach will not clear the EStop with the limit signal hi. Should I try re-installing Mach?
I uploaded a video showing the behavior of the limit switch being triggered. Maybe that helps.
http://www.youtube.com/watch?v=faIeQWPUctUAlso included the Galil debug file and the xml and the last errors file