I think the problem lies in changes.txt located in Loc\Eng. This file has loads of translation entries that override entries in other files such as faction_specific.txt. Just look up the names section and rename everything there.

If you use VI I would recommend using FN_09 etc. for factions, just follow the VI script. Then you won't have the mentioned problem at all and the original campaigns remain playable.

Let us know if you have solved it.

Good luck with it
Duke John