OK - the problem is default valid elements rule set in TinyMCE. Moodle 2.0 is using the full rule set but this Glen's version is using default rules and cuts those tags.
One way to fix this is to upload attached file to your theme folder ( /theme/tinymce_integration/fullrule.php ) and add to your init code for example after row theme_advanced_statusbar_location : "bottom", the folowing tags:
<?php include_once($CFG->dirroot.'/theme/tinymce_integration/fullrule.php'); ?>
You can edit that file - it has one none standard rule for embedding:
+"embed[align<bottom?left?middle?right?top|archive|border|class|classid"
+"|codebase|codetype|data|declare|dir<ltr?rtl|height|hspace|id|lang|name"
+"|onclick|ondblclick|onkeydown|onkeypress|onkeyup|onmousedown|onmousemove"
+"|onmouseout|onmouseover|onmouseup|src|script|style|tabindex|title|type|usemap"
+"|vspace|width],"
that you can take away if you don't need embedding code ( I added that to be able to use embed code in addition to object tags in media plugin altghough it is not XHTML strict valid code )
Note that you should change init code only for that part that starts with
if (!empty($COURSE->id) and has_capability('moodle/course:managefiles', get_context_instance(CONTEXT_COURSE, $COURSE->id)))...
and not the other init code starting with else... unless you want to allow students to add forms.