I'm experiencing juddering issues when playing certain, not all, MKV files with the H.264 passthrough option turned on on my iPad 3. The issue goes away if I extract the H.264 video track and put it in a mp4 container or if I turn off the passthrough option but I rather not do either of those.
I've uploaded a sample of the mkv file with jittery playback with along with the mp4 version that plays properly. They contain the same video track just in different containers.
Video in MKV container (25.3MB)
Video in MP4 container
Here's the conversion log when I select "Play with Live Conversion" for both files.