Here's an explanation of youtu.be: http://techcrunch.com/2009/12/21/youtube-url-shortener/
Weird, but if you try the links in my previous reply, you'll see the weird one works and the one I copied from your site doesn't. If you go to your videos on YouTube, click "Share" and check "Short URL" to see what you get. Don't know if this would have even helped your iPad issue, but thought I would mention it.
The Sliding Notes plugin works very nice for the format of your page. One thing I noticed is that when you slide a running video closed, it keeps playing. Does the plugin have an option for stopping the video when you hide the screen? I only mention this because someone might open a video with silence in the beginning, then slide the screen closed without stopping the video, only to have it continue playing while trying to view a different one. Some visitors might not be able to figure out why the hear 2 lectures playing at once. The few I looked at all had 9-10 secs of silence at the start.
I've been trying all the different plugins for playing videos and there always seem to be one thing that I need it to do differently. I'm going to tinker with Shadowbox JS a little more.