We also had a problem with flash movies in front of the menu. In IE 11 with SharePoint 2013, we could fix the problem as follows:
We add the content editor web part and edit the code. We insert an object along with the ms-wpContentDivSpace class:
<div class="ms-wpContentDivSpace"> <object width="800" height="500" id="flash1" data="https://www.youtube.com/embed/YouTubeID" type="application/x-shockwave-flash" wmode="transparent"><param name="movie" value="https://www.youtube.com/embed/YouTubeID"/><param name="quality" value="high"/> </object> </div>
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