Please make sure you are using these settings in your encoding: http://support.jwplayer.com/customer/portal/articles/1403635-media-format-reference#video/. Some browsers are more stringent than others about encoding requirements. I typically use Handbrake (free on Mac) to encode video files.
Here are a few screenshots of my encoding settings:
ffmpeg is also a great solution to properly encoding h264 mp4’s -