Well, that did not help the issue at all. But I did find a work around.
I am very green to Mach3 and I am afraid I've been a bit tainted to reprap's 'G code' as it was my first real exposure.
It does not seem that you can set a single axis to work using incremental distances, which skeinforge supports on the extruder axis. After executing G91 A it wanted to treat all axis as incremental.
So digging into skeinforges dimension.py I found where it zero'ed the extruder axis.
elif firstWord == 'M101':
self.addLinearMoveExtrusionDistanceLine( self.restartDistance )
if not self.repository.relativeExtrusionDistance.value:
self.distanceFeedRate.addLine('G92 E0')
self.totalExtrusionDistance = 0.0
self.isExtruderActive = True
and changed it to this
elif firstWord == 'M101':
self.addLinearMoveExtrusionDistanceLine( self.restartDistance )
#if not self.repository.relativeExtrusionDistance.value:
# self.distanceFeedRate.addLine('G92 E0')
# self.totalExtrusionDistance = 0.0
self.isExtruderActive = True
Now the extruder axis never resets but keeps accumulating through the print. Couple of test prints later and the results made me a happy boy.
So thats the work around for now in case some one else needs it.