Hey Guys,
I just installed the player and tried something similar, after a few attempts i just went ahead and installed the “Widgets on Pages” plugin, then just dragged the jplayer widget to the widget i created. In my template I added <?php widgets_on_template(“you widget name”); ?> so my new side bar could be created anywhere in the template and it worked perfectly. Try this as an alternative, as for just that short-code in the php, i dont know why it’s not working, maybe because the plugin might be failing to load the the js script it loads in the footer?? :~}