Found a FRED error in Switching off the Light. I successfully escorted the two transports to the station, with about 30% hull integrity each. The mission then told me I completed one of the primary objectives. As I was destroying the gunships, one of the transports was destroyed. As a result, all the allied ships pulled out. I managed to complete the mission, but in the debriefing, it tells me that the mission was a great success, then two paragraphs later, tells me the mission was a failure.
Thought you might want to know. Easiest fix might be making the transports invulnerable after they dock.