I have only noticed this with Star Trek episodes. Handbrake sees the whole episode when i load the source, but then when i go to watch them after they are converted some times 1-5 minutes are cut off from the end of a episode. Some times they end right as the credits start. I've tried 0.9.3, and 0.9.2, and i use the xbox 360 preset. The only thing on the preset i change is the crop. It tents to crop 1-6 on the video.