Mainly, the answer to your question is:
IE is really not a very good browser.
Now that being said and the fact I am not at work I will take a closer look. My guess is it has something to do with the way you have embedded the Flash file.
I will see what I can find out.
<edit>
Okay had a look and (to me) this is very confusing. Now I had a look at your sources and the 3 different css you are using. First a couple things I noticed... you are defining a <div> with the class of "container" yet you never define .container in any of the CSS. Now as far as your problem with the index page.. I did some digging and research 'cause this problem was new to me as well, but I think it stems from having Flash, tables and elements on one page and just the tables on the other. (Meaning it is not just Flash causing this).
In your IE fix css you declare that header and footer use the "static" position, which normally is fine, but your Flash doesn't take up the whole page like your content tables do on the bio page. you can see
the position definitions here. I would try changing that to absolute (even if this means you need a fourth css (iefix2.css for example) just for the index page.
You see, as your table on bio.html fills up all the middle space, your header and footer are pushed (static) to the edge of their container space, since the Flash doesn't stretch, the static area is larger and the header/footer sit "where they are defined" which is NOT at the very beginning or the very end of the page. Does that make sense?
</edit>
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