A few minutes ago I joined a space encounter, selected an enemy ship, and my trusted Escort started to automatically align itself toward the enemy, so the only things left for me to do were to fire weapons, regulate shields and use BO skills. Weird.

I asked around, and someone else said to have had the same experience, but for him or her it ceased to work. Not in my case however, it stayed active until I left the game.

I'd check the Options menu, Controls tab and see if somehow the controls reverted to "Camera Follow Target" as opposed to "Free Camera"

That's about the only thing I can think of that would affect that.

If you do most of your steering with both mouse buttons, you'd end up headed for your target simply because the camera's always pointed at it.

Right clicking on an emeny will target them, align your ship to it and attempt to fire all weapons at the same time. Works for both space and ground combat.

If you double click an enemy I believe it will align to them and max out impulse.