I have located the error.

It seems that, although CA alpha-layered all the Barbarian and Eastern portraits, it neglected to do so with the Roman and Greek (have not tested others).

So before you go through the Roman and Greek portraits, picking and choosing, and renumbering over 478 images and then doing the same for the old portrait counterparts (let alone the rogues and civilians too!) do be advised that you cannot then resize them and have them look right in-game :(

Gah, another huge time-consuming task for me...