I gave my Klingon scientist a last name to represent what house she was a member of, but then, that is all she was ever being called, but now it will not let me get rid of the last name. I keeps saying "a character already has that name" even though the character with that name is the character i am trying to change the full name to.
Hmmmm.....I'm not sure what you're encountering precisely, but I've had that experience before. I named my char Sul'jin and then added "son of" as a middle name and "Gon'dr" as a last name in the full name editor - ended up everyone calling him "General son of". lol
Anyway, from what I understood from you post - the full name you're using is only edited in the in game slots on the character once you already had it created, right? You didn't use the full name as the official character name, right?
If I'm right, then it's weird that it doesn't let you change the name for EC again. Try typing the same name in the 'last name' slot, it may work as a workaround or try playing around with the arrangmenet of firs/middle/last name.