The *HTML* panel <http://getfirebug.com/wiki/index.php/HTML_Panel> is a live view on what is shown inside the browser. It does *not* show the original HTML source. Though it doesn't change tags by itself. I assume you have Flashbug and/or other Firebug extensions installed, right? To check if they are causing your problem simply deactivate them and see if something changed.
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