When I had this issue, it turned out one of the turrets was sucking WAAAAY more power than it was supposed to. never figured out WHY it was, but it always had some messed up flux going on with the power bar on the right side when i midle-clicked and got into it.
I ended up rebuilding the entire thing from scratch and the NEW version worked "fine" after I built it to be self-powered, the base self-powered+enough to power the guns, then docked it to the mothership.
That "fix" isn't ideal since the relatively heavy-and-useless-once-docked reactor system seemed to be what "fixed" the crazy-strange power draw.