I'm just playing FreeSpace 2 after many years. I remember I had gotten up to Captain or perhaps Commodore by the end of the campaign.
After completing the first 3 missions, I had a negative score of -63. This was despite destroying the 2 cruisers (Fenris and Leviathan classes) in the 3rd mission single-handedly with a fighter before the Psamtik fired a shot at them (I destroyed the Glorious before it arrived and the Impervious before it had fired a shot). Checking the stats confirmed that I had gotten both kills. I lost all my wingmen, who were protecting my fighter. I re-armed 3-4 times during the mission. I did cause some friendly-fire hits in a previous mission - I don't know if I destroyed any friendlies. However, I feel that the re-arming is causing too much of a score reduction - I don't think this was the case in the original FreeSpace 2.
I, then, restarted the campaign with a new pilot. I skipped the first 2 training missions, but did the last training mission to get the Wings medal. In the first mission, I got the kill on the Belisarus (I didn't actually take it down by even 1%, but I got the kill). The weird thing is that it shows my "Score from kills only" as 860, yet my "Current score" shows 315. How can my total score be less than the score from kills only? I'm concerned that something might be broken and that I won't be able to progress through the ranks at this rate.