I downloaded Handbrake last night and tried to convert an .mkv into a mp4 (using the AppleTV 3 preset) and i try to play the video today, and the sound works fine just the video is all choppy. Any ideas on what happened/how can it be fixed?
Depending on the codec used in the MKV file, it might not need to be converted with Handbrake, maybe just remuxed, much quicker.
I'm not sure how often Apple updates QuickTime on the PC (or if you have the latest version?) but IIRC the settings used in the equivelent settings used in the AppleTV 3 preset gave QuickTime on Mac some problems in 2010/2011?