I've been converting h.264 mkv movies to mp4 to watch on Apple TV for almost a year, and in the last month they've started ending up jerky, like it's dropping frames or something. It happens when I play them on Apple TV or on my iMac. I'm using the Apple TV setting on "Go Nuts" in VisualHub, and also tried it on High quality with the same results.

I tried removing VisualHub and all it's preferences and starting from scratch with no luck. I've ensured it's using the same framerate as the source video. I don't know where to go from here. I've converted some using HandBrake, but it crashes on probably 2/3 of the videos I've tried to convert. Any ideas?