The NPC mod in Fixt 0.81a does not work properly. Your companions level up at the wrong levels and two companions never level to 3 at all. I've attached links to fixed scripts on the main page. The standalone NPC Mod 3.5 also doesn't work right but I didn't fix the scripts for those and these will not work in that since Fixt changed the global variables.
Vault-Tec Labs