Let me guess. You played the FS1Port then simply went to the campaign room and picked the Freespace 2 campaign and now it's not working right?
Well the problem is that the entire FS1 campaign is run via the FS1 Port mod. FS2 is a completely seperate mod so even though it's visible in the campaign room menu it's not actually playable.
To run FS2 you need to quit the game, run the launcher and choose the mod tab. You'll notice that your currently selected mod is the FS1 port. Simply choose the mediavps folder and FS2 (with SCP enhancements) will now be your selected mod.