yes, i know its an odd thing to be irritated about, but i occasionally drop them into a game as a npc for the heck of it,and was wondering what causes that bug/glitch?

Check the faction file, 'sid.txt', It should look like it does in the screenshot below. If the Gaians come up any where, then change it appropriately. If everything is fine, the check 'sid.pcx' which should look like the second screenshot. If this shows as the Gaians, then the Firaxian graphics have somehow been overwritten (perhaps by the faction editor?)
The other .pcx files ('sid2.pcx' & 'sid3.pcx') should also show the Firaxian graphics. Finally, check that under custom factions in 'alphax.txt' there is something like the 3rd screenshot.

Good luck, and if all of these files seem to be correct, reinstalling SMAX may fix the problems.