There's one mission that has that bug on occasion, caused by a corruption of the auto-save file. To clear it, fly sim mission 6 or 7 for a few seconds (no need to finish the sim mission).
If that doesn't work (I have yet to hear of it not working, personally), go into the main Prophecy directory and delete the file autosave.gsw, and use the mission history terminal to select the mission before when you play next.