Yes, I understand what you are saying, though I'm having trouble relating it to what is happening here, so let me put it in other words and see if your rationale makes good walking around sense.
1) I move to a certain x,y coordinate on my table. I do this at a rate of 20ipm. Nothing fancy, just good old fashioned G1 motion of 2 axis at once. That part is, frankly, irrelevant, but it lead up to the next move.
2) Milll arrives at destination coordinates. Lookahead tells it the next move is back in the other direction on both axes. It has to make a very small move on the x axis, and a moderate move on the y axis, and its being asked to do it at a G0 rate and using backlash compensation. It initiates a backlash compensation at a snails pace, because i have commanded it to move at 0.1% of 90ipm, which should be .9ipm. This is the meaty part of the torque curve for a stepper motor. Only thing that could be better is if the thing was just dead stopped. Mach 3 actually commands this backlash compensation to happen FIRST in the y axis, THEN in the x axis. Again, this is happening at a snail's pace. I could paint a scene of this on a canvas its going so slow.
NOTE: there is no RACE to get either axis to its destination. You mention that the x axis move being a short distance being a problem becvause it doesn't have "TIME" to get there. In reality, it has how long it takes for the y axis to make a large traverse, which is ample time to move the x axis a short distance.
3) what happens next I have no explanation for. The y axis then lurches forward at a speed far greater than either the backlash compensation speed or the acceleration rate are set for. The x axis is already backlash compensated, so there should be no 'rush' to get anything anywhere. It just lurches forward in the already compensated direction.
4) The rapid move should now be ramping up. At anything other than a glacial pace, this will fail and the Y AXIS MOTOR will stall, so long as the aspect ratio is high. Mind you, I can rapid all day in any direction in any combination of axis so long as the aspect ratio is not high.