hi,
i've triied adding
iframe[id|class|title|style|align|frameborder|height|longdesc|marginheight|marginwidth|name|scrolling|src|width]
into the mce_valid_elements var (in assets/plugins/tinymce/js/xconfig.js) and it works without any problem, works too when i add it to mce_extended_valid_elements var
i do all this directly in the js file, a liitle simpler, faster and more reliable
i've tried with a youtube video to see if there were any peculiar issue with those, nope, works like a charm
your problem may come from the fact you haven't included frameborder in you snippet when youtube uses it for their embedding code, grab the whole stuff i wrote above, you shouldn't have problem any more
have swing