That's a first generation mod.ini from before I made the changes. I didn't know anyone had actually listened to me back then so I didn't think changing the names would ever cause anyone any problems
As for the cause of your problem you've got me really stumped here. There are only two reasons I can think of that the media VPs will work in the main folder but not in the mediavps folder.
1) You've supplied the wrong name in the mod.ini
2) You've got a rogue table file in mediavps\data
So lets do this properly. Use the new mod.ini. Delete mediavps\data completely. Run the port and see if you're getting the new Fenris in the techroom. (CTRL + SHIFT + S if you don't see the fenris on the list)
If that doesn't work open up the mod.ini in FS1_Port and change this line
secondrylist = ,mediavps;
into
primarylist = ,mediavps;
and run it again. You shouldn't get the FS1_port running properly now. If you go to the techroom and press CTRL + SHIFT + S you shouldn't see any of the FS1 era ships like the Anubis etc. If you do we're looking at a misnamed folder or some kind of code problem. Put the mod.ini back the way it was and double check you have the folder names correct.
EDIT : If you change the ini while the launcher is running it won't spot it. Restart the launcher every time you make a change just to be sure. (Or simply select no mod and then select the FS1_Port again. Whichever you find easier).