A few things:
A) Was using the same Shivan pilot for every campaign. Didn't know you couldn't. Creating a new pilot would've been the same as restarting.
B) Derelict and FSPort had stopped working, they were both giving me useless weapon loadouts that I couldn't change during missions
C) For some reason Turey's installer was crashing when I tried running the updater. The installer seemed to be working fine so I just figured I'd start from scratch
A: It's recommended to make a new pilot for most bigger campaigns using a lot of modifications, or at least clone an old one (then you don't need to set up controls config etc. every time). Usually I just play with old pilot, though, and if I encounter problems I make a new one and restart the campaign. They aren't usually that long.
B: So, just wipe the Derelict and FSPort out of circulation, clean up the root data folder (create backups first, though) and re-install Derelict and FSPort...
The data Freespace 2 retail uses is inside the VP files in the root FS2 folder. They are read-only files for the game's point of view and thus they are not usually corrupted by the game.
In fact, Freespace 2 Open will start to work if three conditions are filled:
1. Retail VP's are in a folder
2. fs2_open_r.exe and Launcher.exe are in the same folder
3. OpenAL is installed.
Fire up the launcher, do some settings if you like and run the game. It runs fine, I just tested it. Obviously, the movies are missing in this configuration, though, but as they are separate files it's easy enough to backup them, too - they reside in data\movies folder (or on some cases in root folder). The game will then set up the root data directory as the game is played - the first directory it creates is data\players\single (or multi, if you create a multiplayer pilot), then as you proceed into missions it will create a cache and so forth. So it's rather easy to "re-install" FS2 without having to re-download everything from the scratch in any case and then be more careful with what to install and where. Every mod to their own mod folder as a general rule.