Good response Josh, I wish more plugin developers were on the ball like you! :)
I don't know what was going on with your plugin, there were some alerts in red (I think) at the top of my admin pages bugging me to go do some settings of the plugin, so I went and selected the "Default" setting just to shut it up, perhaps that's what checked the box? To be honest, I have no idea. From my point of view, I don't want to see messages, or have to select "settings" I just want to activate a plugin and have it work. The thing is, not all of us are technically savvy, we are just some monkeys that type stuff up and publish it, and anything that requires us to make "settings" before we can use it will just get in the way and frustrate us poor monkeys. :)
I did solve the issue of imbedding the You Tube videos, it was a Pretty Photo plugin causing the issue. It has a "settings" page with some check boxes checked by "default" that basically stripped the code that would imbed the video. I guess the idea was to place the vids inside the Pretty Photo box, but it wan't doing that, and I guess the author never checked to see if it actually worked. I would chew him a new one, but, like so many authors I have seen, he has since abandoned his plugin. Un checking the boxes for video imbedding in the plugin solved the problem.
When I first saw your plugin I thought it was brilliant, and my look at it again, but right now this monkey must type so he can get paid! :) Thank you so much for following up!