I've encountered a bug, atleast using the KSPI plasma nozzle paired with a tokomak fusion reactor. I have a ship with a vtol lander attached to it, with the vtol engines pointed perpindicular to the rest of the craft. Despite them being turned off, they seem to receive priority over the plasma nozzle which is enabled. The craft gains no thrust from the plasma nozzle under timewarp, but the vtol engines (which are just the restock twich engines) will cause the ship to move undertime warp if I activate them.