Hi,
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.
https://docs.google.com/file/d/0B9j6FQo4cSQFRnl3RjJxUkxnR0E/edit?usp=drivesdk
https://docs.google.com/file/d/0B9j6FQo4cSQFcE92aEZSMVprdVU/edit?usp=drivesdk
https://docs.google.com/file/d/0B9j6FQo4cSQFNHVlQVgwb3dWWmM/edit?usp=drivesdk
https://docs.google.com/file/d/0B9j6FQo4cSQFWmNNbzZLUndNNlU/edit?usp=drivesdk
https://docs.google.com/file/d/0B9j6FQo4cSQFUzdUWUw3R21nMFU/edit?usp=drivesdk
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.