Step/Direction puzzle

I'm trying to set up a system with 3 Gecko 201's to drive a Sherline
Mill. To drive the steppers I'm trying out CNCpro and Supercam. When
I tried these on 2 different laptops I find that the X axis motor
only turns in 1 direction when jogging using either piece of software
y direction works fine. If I try it out on a 3rd laptop I can get
CNCPro to work but not Supercam - it fails with the same problem only
one direction on the x axis.

I am at a loss to explain this since I'm setting up the pin out's the
same in the software on each machine. It seem's the x direction
signal is not being asserted on 2 of the 3 machines. The problem
seems to follow the software x axis config eg if in Supecam pin 2 and
3 is x step and direction it only turns the stepper one way. If I
assign the y axis to 2,3 the same motor will turn in both directions
but the motor attatched to 4,5 will now only turn in one direction.

The Gecko's are being driven at 48 volts current limited to 1 amp.

Has anyone got any clues to check out? I'm now doubting my own
sanity :-)

Richie