I am trying to understand the issue. You are writing a post and you want to include a video. You copy the code like below into the post by clicking on the 'html' button pasting the code and then updating. Correct?
<object style="height: 390px; width: 640px"><param name="movie" value="http://www.youtube.com/v/iSdESmf_Ar4?version=3"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://www.youtube.com/v/iSdESmf_Ar4?version=3" type="application/x-shockwave-flash" allowfullscreen="true" allowScriptAccess="always" width="640" height="390"></object>
If you are trying to update the tinymce editor in BE the file you would want to add the above mentioned update is in the admin folder called tinyMCE.ascx.
I am able to add the above code no problems and I have made no amendment to tinyMCE. So, that is why I think I might not understand the problem.