My memory of Batman Begins in the theater from 2.5 years ago is that the colors showed very little difference, if any, from the Bluray. The triple-feature screening at the Cine Capri I attended was of all three films in 2.35:1 ratio throughout.

Given the information and anecdotes in this thread, I'm starting to think that the Imax and 35mm versions may well have had different colors from each other, due to the simple fact of their having been made at different times with different processes and equipment, most of which were analog and therefore not capable of being duplicated exactly with no change every time.