Pardon me for asking, but have you checked that your Microsoft browser is not at fault in that it could be in Compatibility Mode? This can throw quite a few themes out.
To check CLICK on F12 ( that's Function Key 12 on your KeyBoard)
In the popup window you will see midway across the middle of your screen two tabs telling you which mode it is in. These should both refer to Internet Explorer 9 for Standards as well as Documents. If you find that it is IE9 Compatibility, or IE8 Compatibility, or IE7 Compatibility or heaven forbid IE7 Quirks Mode, then just click on the one that is for IE9, assuming too that you have got the latest in IE9 or maybe you should upgrade to IE11 which is far more Moodle Theme friendly.
Also, have you thought of complaining to Microsoft to ask why it is that their browsers are years behind the rest. In fact if you did they would tell you, as we do, to upgrade!
It would be perhaps better too, if you added FireFox as an alternative browser for your students, as that is pretty good and works on older desktop computers like XP.
Hope this helps?
Mary