Ok a little nerdish here, but I had this problem with having the JW FLV Media Player and a NextGen Gallery on the same page. The playlist and playbutton of the flashplayer was showing through the modal window when showing the large pictures of the NextGen gallery.

This only happened in FF on mac … Safari on Mac, FF, IE6 and IE7 on pc did not have this problem.

I solved it by adding
$output .= ’s’ . $videoid . ‘.addParam(“wmode”,”opaque”);’ . “\n”;
in the plugin editor.

Put it after
$output .= ’s’ . $videoid . ‘.addParam(“allowscriptaccess”,”always”);’ . “\n”;
and it should work.
It is still a little querky, as the flash player comes throught the modal window when you page through the pictures in modal mode, but it is definentely better than having a big playbutton in the middle of all your pictures.

Hope someone can use this – and thanks to Dan!