I don't have any inside or official information, but I believe the problem to be this: The guns are simulating recoil by moving back several feet after they fire. They return to position quickly thereafter to position it for another fire. The exit you are trying to get through is physically blocked by the guns, but when they recoil space opens up to allow you to pass. Once you proceed the next gun is in the way and you have to stop. This puts you in the way of the gun you just past which is resetting your position. You try to go backwards but the gun behind that is now in your way preventing backwards movement. So, the jerky progress forward and back.
Since the car you are travelling in is "trackless" It could be possible for a malfunction of sensors to allow your car to be inappropriately positioned and be in the way of a resetting gun. I do not believe Disney would design the ride with a collision point possible, but I do not know how far they take it with the simulation.
My guess is that it is a software / hardware issue where the movement of the car and guns is not synchronized properly. And it could cause the entire ride to stop. So, it is just easier to run it in B mode. However, it seems really silly for the jerky motion with stationary guns.....
IMO totally fixable given enough time and resources. Maybe the existing programming just needs some updating too....
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