MechJebModuleRoverController.cs does:

if (s.wheelThrottle != 0 && (Math.Sign(s.wheelThrottle) + Math.Sign(curSpeed) != 0 || curSpeed < 1))
{
brake = false; // the AP or user want to drive into the direction of momentum so release the brake
}

kOS can produce a situation where what kOS calls "wheelthrottle" is 0 (and the wheels don't, in this situation, provide drive), what kOS calls "ship:control:pilotwheelthrottle" is non-zero (the pilot has the throttle non-zero), and the brakes are on. (This is in the context of a kOS script which brakes on overspeed regardless of what the human at the controls is doing).

MechJeb then immediately turns them off, which is not the desired behaviour.

I submit that a MechJeb option to turn this behaviour off would solve the issue.