So I decided to stop using VisualHub/HandBrake to re-encode my MKV's here as I figured out that I could just switch the container with a mov-container (by using Save As in Quicktime) and add it to iTunes that way. Then I have no quality loss from the original MKV and it's A LOT faster than actually re-encoding the file. But now it won't transfer to the AppleTV, even though both the resolution and the fps is within accepted range. Is this a matter of the bitrate of the video? Or is there something else going on? (It says it's H.264 just as the converted ones does). Will hacking my AppleTV fix this in any way? Or is it iTunes holding back the file? Is there anything I can do to get this working?