Hmmmm, I have run into a rather odd bug.
I start mission 1, and what do I see? I got no primaries, whatsoever, and only a bay of Tepmests, that's what. I installed the file where it's supposed to go, so I don't think that's an issue. I haven't downloaded the patch file or whatnot yet, so that may be it. I am also running vanilla FS, as I just recently re-installed FS on my machine and have been to lazy to download FSO again, but I don't think that should cause an issue, as the readme says it can work in vanillia.
EDIT: I just got the update file, and it still is doing that to me.