[Suicide Junkie]

Weapons in SE4 do not require supplies to fire, though they do spend supplies.
Combat movement does not use up supplies either, but should require them.

So it just looks like the afterburner is buggy, and should not provide extra movement when supplies are depleted.

Try putting one engine on the fighter, and see if it slows down to 1MP when it runs outta supplies (use the most ammo-draining weapons you can find)