So I beat the mission to protect the Armegedon (after the 30th try...) and I engage the autopilot to return to the Hermes only the screen shows me and my wing mates flying away from the Armegedon... and away, and away, and away... and never comes out it. Has anyone else had this problem?
Not that I know of. The ending cutscene event must have misfired for some reason. It's really bad luck for it to have happened on that particular mission.
I would recommend either killing yourself 5 times to skip the mission, or download the mission attached to this message, unzip it, put it in H:\Users\<user-name>\Documents\Volition\Wing Commander Saga\data\missions, and play through it again, with allied capships invulnerable this time (yeah, I lost my patience after the 20th try) (sorry).