I’ve been struggling this issue almost of the time when tried adding youtube iframe videos especially below the menus. This problem mostly seen on IE. You found it weird because it looks good on Firefox and Chrome but when checking to IE and urrrggghhhh, why the hell it overlapped the menus.
The solution to this issue is to have
<param name="wmode" value="transparent" /> within the
<object> tag. But as this is an YouTube video, and we are using iframe to embed the YouTube video, we can’t add
<param name="wmode" value="transparent" /> to the code. So the perfect solution is, tried adding ?wmode=transparent at the end of your youtube URL.