I think it's actually partly because you're really not intended to change window focii once you're in game. As such it'll snap back to your default brightness once you change windows and the KotOR II settings just won't override your normal desktop ones.
My $0.02 anyway
From what I've seen this is deliberate and only happens at a few workbenches...
, usually where the Exile doesn't happen to be in the party.
Try another bench?