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I insert flash with dialog box. Inserted code is:
<p><embed type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" src="http://domain.xx/address" play="true" loop="true" menu="true"></embed></p>
that's a known problem: http://dev.fckeditor.net/ticket/382
The <embed> tag is deprecated, and should no longer be used. I know that popular sites tell you to use it when they give you the code, but all that you need from them (Google Video, You Tube, etc.) is the movie source, and the dimensions. Here is an excellent article on why and how to show video on a site without the old embed tag: 'http://www.alistapart.com/articles/byebyeembed/'.