How to change order of javascript files in Drupal 6?
If you look at drupal_add_js() and drupal_get_js(), you will see the details.  Unfortunately, module_invoke_all() or it's cousins, don't get called, which means there are no hooks.  Boo.  A related issue is that when you aggregate, you loose the ability to do string manipulation (eg, explode, reorder, implode).

The best way to handle this is to alter the weight of the JW Player Module.  One way to do this is to edit the {system} table and edit the weight column value.  With the weights, lower numbers run earlier, higher numbers later, and where there is a tie, they run alphabetically.  Make sure you clear cache when you do this.  See Change module&#39;s weight - by module or manualy for some more details.

If this doesn't fix the problem, then the JS files aren't being added by the same hook.  I am not sure what can be done it in this case w/o hacking the module.

A total sledgehammer approach would be to not include the your code, but to add it in the theme's .info file.  This should add it after all modules.