I had a similar problem - I think it has to do with the scripts for randomizing certain soldiers gear. (Edit: like you were thinking - yes there is a script that puts certain randomization into certain troops gear)
The way I got around this - was by adding a new troop type, and adding the upgrade path to that troop to one of the existing ones (I used the special "neutral fort" guys to make my own custom Imperial army)
So, Sado Exiles used to only go up to "Sado Returnee" - now they go Exile -> Returnee -> Imperial Soldier.
Basically - instead of just editing an existing soldier - they now upgrade into a totally new type (Which is not included in the randomizer script)
Really easy to do with MBEdit.