AFMUnits just shut down the module they are working on which is why they can't fix the power pack and it is a bad idea to use them on thrusters or FSD while in cruise.Does the AFM work in the background or do you have to completely shut down your ship first? Every time I rebooted the same NPC pirates kept attacking me.
The Reboot/Repair option on the ship tab in the right hand window shuts down everything at once for what seems like an eternity.