I'm at work so just a quick more hints as I cannot spend much time:
1. ALWAYS use a new pilot for new campaigns/mods. (Sometimes stored old data from older ones raise problems).
2. Freespace2 SCP folders cannot have spaces ("Media vp" is not a valid name and a common problem could be "Program Files\Freespace2\". If this was your case, make a full REINSTALL of FS2 in "c:\Freespace2\").
Just a hint about how I've got my installation:
1. As I don't use retail FS2 version anymore, I've got media vps within FS2 main folder.
2. I've got FS Port v2.3 and v3.0, so I've got two folders for FSPort 2.3, one with its own different files and one with the ones that are shared with 3.0 (***_fs1.vp and so on except sparky).
3. I've got LS Nebulas in its own folder. (They are optional).
4. I've got BR_STL.vp, BR_STLv.vp and WeaponsPack.vp in MOD_STL folder (with its MOD.INI).
So my SecondryList is more or less (I don't remember exact names):
SecondryList = ,FSPort2_3,FSPortShared,LS_Nebulas;