After using some really outdated missions for a while (because of the music), I decided to see what the new missions were like. So after painstaking going through every single mission and changing the briefing and in game music to fs1, I decide to replay the campaign from the beginning. Everything was fine until........
That mission where you capture McCarthy. For some reason, the Horus, the Isis, and the Osiris ALL show up as Ulysses fighters. I ignored it and went onto that next mission. When the first wave of Vasudans shows up, the Osiris is a Ulysses (at which point I quit).
WTF is going on? I swear I didn't change anything other than the music. Everything else shows up just fine (so far).