I am very interested in this project and have been trying to follow along myself. I love the movie but have hated the blu-ray due to edge enhancement and the color timing. As I tried to create the media to follow along I ran into a few problems. I am running a Mac but decided to bootcamp in order to import the VC1 files from the Blu-Ray, and editing them back on the OS X side. After exporting both the BB Prologue and Dark Knight video streams I noticed two major issues.

The color in the both clips is different from their original sources. It looks like maybe the original has a slight a very slight shift towards green/yellow areas.
At around 2:53 in the Dark Knight stream green frames start to appear during every encode attempt.

These issues have occurred independent of what codec was being used, UT QT and ProRes being the major ones I am testing.
Note that I am using Adobe Media Encoder as that is what is available to me cost free right now.