Wow! Great thread! Thanks so much for all the wonderful tips and information to everyone.
I'm having a small problem with the Star Trek blu-ray. After I rip the movie using AnyDVD HD, muxing in tsMuxer and transcoding in Handbrake (0.9.4) GUI, everything looks and sounds fine in QT and VLC. When I put it into iTunes to view on ATV I start getting heavy blocks and artifacting. So bad that when a scene changes occurs (example: Paramount opener to Bad Robot) some of the original scene still lingers as the new scene plays. My Apple TV is wired to my router and HD movies I've downloaded from iTunes play just fine.
Here are my specs for HB:
Codec: h.264
CQ: 59% (RF: 20.75)
Pic Size Output: 1280x528 (after auto-cropping)
Audio: English (AC3) (5.1 ch), AAC (CoreAudio) DPLII
I've tried setting Detelecine to "off" and "default" as well as Decomb. Everything else is left at the default settings.
I've gone through the whole process a couple times as I thought that maybe my rip from AnyDVD was bad but it still occurs. Again, everything looks fine in QT but jacked on Apple TV.
Any thoughts or suggestions would be greatly appreciated and thanks again for the bounty of info!