I installed the JW Player and it is working fine with the theme. I just used a shortcode after creating a playlist
[jwplayer player="2" playlistid="3540"]
Here are a few screenshots that might help you if you are doing something wrong.
Note that the plugin supports only few audio and video formats.
If you are still facing the problem, then please mail me a temporary login to your site and I will take a look. Thanks.