First off —
When including Javascript, use a function hooked to the init action in functions.php. See:
http://scribu.net/wordpress/optimal-script-loading.html
Secondly —
The CSS for the BP bar is being effected by something in your theme. If fixing how your Javascript is loading first doesn’t fix that issue, try selecting that object in Firebug (Or Chrome’s developer tools) and seeing whether any files other than style-adminbar.css are effecting it. It’s likely you have some reused CSS class names somewhere.
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