You win the weirdness prize for weirdest problem with my mod. I don't have a problem with the frigate and science vessel being the same but it seems that I purposefully removed the carrier from the game selection, probably to avoid a bug. It can be used in the simulator though.
I made some changes, you can use the carrier in the military mission and it has been removed from the intro screen.
http://www.filegone.com/s4ci