Are you playing the files from the PS3 or streaming them? The PS3 will play quite a bit of H.264 formats if played directly from the PS3 (unfortunately it won't play the Apple TV preset). I've had almost zero luck streaming files to the PS3. I'm looking for a preset that will output files that will play on xbox 360, ps3, apple tv, and my pioneer tv, which will also play media files. So far the PS3 preset with some tweaking has been the best but I haven't tested it on an apple tv yet.