I have experienced this often. When updating a page or post for any issue, the youtube code simply disappears and I have to go back in and restore a previous page.
I just had the same issue happen to me today with a Facebook Fan Box. When updating text on the same page as the embedded fan box in the visual editor the facebook code was lost when I updated the page. I had to go back in and restore the previous page.
Is this a wordpress issue, server issue, or other issue?
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