FSPort files contain all necessary files, so unpacking them is not needed. Further, the files don't need a sub-folder at all, they _all_ exist in the Fs1Port folder. All of them. Try renaming Fs1Port to fsport. Also, you should run greater than 3.6.7.exe.....while the fsport files are made for 3.6.7, later versions offer better.
Also, while not necessary, the mediavp's are also a good thing to have, and they all should go into the Freespace2\mediavps folder.
All new (Post 3.6.7 builds) can be found
In this forum category. RC5 has a problem where shields don't recharge. Grab the multi_test.rar (Unnoficially RC6, downloadable in the Release Candidate 5 thread) or any redmenace build of 20060712 or later.
*EDIT*
I also rename 2 of the files to ensure ascendancy (make sure they will get used properly).
I rename fsport-fs1_training.vp to fsport_fs1_training.vp & fsport-missions.vp to fsport_missions.vp.