I've recently upgraded to Handbrake version 0.9.5 and I've started encoding using the Apple TV 2 preset. I've noticed that it seems to cause lighting issues with the finished product. Throughout the movies, some scenes appear dark and then all of a sudden light up. Then it darkens again. Anyone else having these issues? UPDATE: So the issue isn't Handbrake. It's a particular Blu-Ray movie, and Quicktime/iTunes. The final product plays fine on the Apple TV and VLC. It's only when I play the movie in iTunes or Quicktime that the lighting issue occurs, and I'm not sure why. I've yet to test it on my iPhone.