Hi, ALL
Don't know how I missed this Post, Been sidetracked a little with threading and other issues hear, Look's like you all need another opinion or two.
Nickle989, I think "Techsol" Hit the nail on the head as you seem to think also. So you should be on the way to resolving the Problem. I usually recommend setting all the Motor Outputs, Dir/Step Low-Actives to All the same State (checked or X), But in your case that may not be possible. If any of your motors run backwards you can use, Home & Limit's, "Reversed" to change there direction without re-wiring the motors.
To late for further comment, Maybe tomorrow.
Chip