One thing that can mess up the player is mootools. It can screw up the layout of the player slider and volume slider.
If you don't need mootools, don't load it.
Some other extensions or modules load mootools. A great free plugin is Mootools Enabler/Disabler.
With this plugin you control where to enable/disable mootools. MyMuse does not use mootools. It uses JQuery.
The HTML5 jPlayer uses unordered lists for many of its elements and some templates can override the display of lists.
Using firebug in Firefox, or Chrome's debugger, you may be able to determine any changes necessary.