Try adding this to Confluence Admin | Look and Feel | Custom HTML | At the End of the HEAD:
<script> AJS.toInit(function(){ AJS.$('object[type="'"application/x-shockwave-flash"]').append('<param name="wmode" value="transparent">'); }); </script>
No guarantees, but it's worth a try. This is untested as I don't happen to use the plugin you mention.
Edit: See also some other tricks:
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