That's intentional. Brightness adjustments depend on the user's screen, after all, so it saves the unbrightened image. Yeah, this. The transparency of the leaves is defined in a thing called a shader, which is (in Jedi Academy's case) basically a text file that defines the material. A single broken such file can break other ones as well, so chances are you have a custom map/model/... that comes with a broken shader, resulting in broken trees and who knows what else.