Hello!
I encountered the same problem. I just found out about and did a fresh and complete install of FSO (Online Installer) this weekend. I want to get into the Freespace universe chronologically, so playing FSPort first seems like the logical thing to do. I configured everything according to the threads here, created a pilot in the start screen (first and only pilot), selected the FSPort campaign and started playing.
Everything was fine up until I reached Advanced Training 2, where I am being briefed about the interceptor missile, but in the mission my secondary weapon slot is empty. Interceptor#weak is being shown in the weapons room, but doesn't appear in the mission.
I tried a new pilot as Goober5000 suggested - no luck.
I tried editing the mission file like mrduckman suggested and also tried the file he uploaded. But no matter where I put the changed file: /Freespace2, /Freespace2/data, /Freespace2/data/missions, /Freespace2/fsport, /Freespace2/fsport/data, /Freespace2/fsport/data/missions ... it doesn't have any effect.
I'm really running out of ideas here, any help would be appreciated.