I did the worst thing any of us could do, and that is not test IE. Believe it or not I just upgraded to 3.7.7 from 3.6.8 and made the minor functions.php revisions. Around this time I upgraded IE to 9 and never checked my site against it. When I did my CSS did not show up at all. Only the default Power Blog Theme. Second, the Home link does not show up.
I double checked the forums. I double checked my CSS and functions.php file, and I feel I may be looking too hard. Is there a little bird out there who can tell me what the hell I just missed? the site is "http://oldschoolscholar.com .
I am ready for my "duh" moment.