Probably already taken care of, but....

[Duke Atreides]

I did a custom game as Arche Seleukia, versus Pontos, and when I started the battle, my troops were Romani, although still Hellenistic Cataphraktoi. I was still fighting Pontos, the only difference being that my units had the red Romani battle for their unit skins. My apologies if this has already been dealt with, but I just downloaded the mod.

[Kralizec]

Hello Duke Atreides (nice to see another Dune fan )

EB has shuffled around the original faction slots. The Julii romans are now Arche Seleukeia, and Carthage is now the Pontos faction, for example.
From what I read, you haven't installed the patch yet. Go here and follow the instructions. It fixes the banners your units use in battle, not the voices though.