Is there something up with the Power Core on this ship? Sometimes when I'm shooting it will completely drain and never regenerate. When that happens I can't defend myself and when I try to go into cruise I move a -1 speed. Its has a Liberty Police ID/IFF and Charon turrets, but when I undock I don't get any incompatibility notifications.
I guess you are using one of the heavy transport shields that have 100 000 capacity.
The problem is they consume 3000 units of energy per second, when regenerating, which happens to be as much as the whole power generation rate of the Armored Transport.
Try using one of the smaller transport shields.
