If you die or fail the mission five times, you can proceed to the next.
The bug you describe is interesting, but although the jump-in distance changed between FS1 and FS2, it should not have changed in the FSPort. Does Rama wing actually arrive? Rama will exit the docking bay once you fly to the correct spot. Follow the Arjuna fighters to see where the docking bay is. (There are actually two docking bays, one on either side of the ship. Either one should work.)