Don't know why this keeps happening to me...
I played through the game once now, and whenever I attacked or anything, my leader Taril (playing Dark Elder) just came up as the generic Archon. Same thing with the leader of the Sisters of Battle (can't remember her name), it just says Cannoness, and when I hold the mouse over, it just says "commander unit, primary" and all that. Yet if I start with, say, imperial guard, it says General Stubbs.
Also, for Taril and the Cannoness, the updated wargear doesn't seem to register in-game. It will state all the stats on the commander screen, but not in-game.
I've had this happen in Dark Crusade as well.
Soulstorm, incase you didn't know, is a gliched up son of a bitch. It's got so many bugs in it I don't even know. But I do know they have a list at relicforums. They also add to it as they find new ones.
Well, relic forums seems to be down, so this is the next best thing. My email to Atari about this was answered with:
"Wow, we've never heard of that error!"