Try adding:
“wmode=opaque”
as the first GET variable in the url for the youtube video.
(eg: src=”http://www.youtube.com/embed/12345assdfdfdf?wmode=opaque&rel=0″)
Worked for me in a similar situation. This actually works!
Source: http://stackoverflow.com/questions/10700577/youtube-video-inside-iframe-not-hiding-in-safari-5-1