I had an issue where my Suckerfish CSS dropdown menu appeared behind the Flash video. I managed to resolve this by editing line 561 of youtube-channel-gallery.php and added &wmode=opaque as below.
Perhaps you could add options for this into the shortcode.
$content = '<iframe id="ytcplayer' . $plugincount . '" class="ytcplayer" allowfullscreen width="' . $ytchag_video_width . '" height="' . $ytchag_video_heigh . '" src="http://www.youtube.com/embed/' . $youtubeid . '?version=3' . $ytchag_theme . $ytchag_color . $ytchag_autoplay . $ytchag_rel . $ytchag_showinfo .'&enablejsapi=1&wmode=opaque" frameborder="0"></iframe>';
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