Likely protections.
Try watching the movies using VLC Media Player, which is free/opensource.
VLC should be installed in folder root/Applications, not in your home folder/Applications. Also, ensure you're using the same bitrate for Handbrake and VLC. This may also be part of the problem if you are booting into 64-bit mode, or if Handbrake is at one bitrate, yet your media player is at another bitrate.