Autofiring, whether ground or space, interferes with activating other powers. A space example: I'm fighting and see that my sheilds need some regen. I hit Emergency power to Shields & keep fighting only to see my shields keep going down. I look at the power tray & yep it wasn't activated. This affects all powers.
I know this is a problem with the game engine, since CO did the same thing, but please try to fix this.