I don't have any MKV files. I use handbrake for converting DVDs and h264 TS files.What settings do you use for Mkv files then? Thanks
For AVIs and other files, I use VisualHub.
In the picture below you can see the difference between the default AppleTV preset (the one at the top), and my modified preset (the one at the bottom). My modified one generally gets me about 18-23 fps when encoding a DVD, whilst the default AppleTV one gets me about 6-9 fps. I don't really understand what the actual difference is but I'm happy enough with the output generating from my preset.