Since we're on the topic of HandBrake rather than MKV files, I thought I'd throw this question out there.
I have EyeTV recordings, and the QuickTime conversion gives me pitful results. Now, onto my question:
1. When I do this in HandBrake, I crop the video (8x8x8x8, for overscan) and set an output resolution of 688x384 at 1100 kbps bitrate, Apple TV preset with deinterlace set to slower. The source, is an MPEG-2 file. My outputs aren't the best quality - sometimes a bit blocky looking, and the audio is out of sync by a fraction, but noticable.
Is this a known issue, or am I doing something wrong? I know I won't be able to get great quality, but I have ripped DVD's with those same settings and the result is great, just seems to be the MPEG-2 files I have issues with.