I am using FFMPEG to convert a video to .mp4, ,ogg, .webm so that it may be viewed in all HTML5 capable browsers using the video tag
I would try this code first. It is as simple as possible.
Creating mp4 files, minimal number of arguments. Unfortunately, I haven't tested it much.
ffmpeg -i input_file -vcodec libx264 -vpre medium output_file.mp4
To creating ogv files You should use ffmpeg2theora. There are too many problems with ffmpeg.