Video keeps looping when I encode it!

Help! I am making videos for YouTube and have been trying to use my face cam. I record on my iPhone which produces .mov files. I get them to my computer via Google drive. Once I download them I put them through the encoder and switch them to h.264 - the problem is it messes up the video! The video loops a 30 second to 2 minute clip, and the audio plays normally. When I trouble shoot, the video plays fine on my Google drive but is broken when it gets encoded. Any advice?