While that might explain the failure to render the flash, it still does not explain the page being off-kilter or the content of the iframe just not being there. But this might:
http://www.sitepoint.com/forums/html-xh … 43000.html
Joy. Gotta love IE. Could we just lead the masses over the Firefox?
By the way...I guess from what I was reading, the iframe content and the "framed" page need to be the same doctype (or IE forces it...)....easy to do when adding your own content...but not so much when the child content is not yours. Looks like YouTube is using HTML5 and your site is HTML4.
You might try looking about for a long-term solution...but see if this helps for now. Add the following in the "head" of your page with the other meta tags:
<meta http-equiv="X-UA-Compatible" content="IE=8" />
I tend to think somewhere there is or will be a solution as YouTube (which offers up the iframe method to embed the vids) is likely getting an inbox-full of questions and complaints.
...Oh....and I went on this little quest because in the IETester where the vid should be, in IE9, there was just a big white open void.