I just updated to 3.5 and it seems that when I try to embed a video using the shortcode there is an extra blank embed box above the actual video. I have a ton of posts with this shortcode so please look into this.
I am having the same problem but am not using Shortcodes Ultimate. You can see what is happening on a new client install at sportafence.com on the home page. I am leaving the error in place until you have a chance to see the problem. I have to get it down ASAP though since this is a live site. Your immediate attention to this problem would be highly appreciated. Thank you.