Generally they don't put anything in the joomla backend regarding player wmode settings. And its usually up to the dev's of such plugins or module's to offer support for such things.
You will have to modify the code used to install the player.
1st you have to set the player swf to wmode: 'transparent',
Then set the z-index of both the id="player" and of the menu id or class.
This is wmode for the player.
<a id="player" style="display:block; width:520px; height:330px;position:relative;z-index:0;"></a>
<script language="JavaScript">
flowplayer("player", {wmode: 'transparent', src: "/flowplayer-3.1.5.swf"}, {
clip: {
url: "/your-video.flv",
scale: 'fit',
autoPlay: false,
autoBuffer: false
},
plugins: {
controls: {
url: '/flowplayer.controls-3.1.5.swf',
backgroundGradient: 'high',
timeColor: '#980118',
all: true,
tooltips: {
buttons: true,
fullscreen: 'Enter fullscreen mode'
}
}
}
});
</script>
After setting that you will need to adjust the z-index of the menu setting it to anything above 0 Eg z-index:10 or something.