You have lots of validation errors in your theme code, starting with the fact that these three lines:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
need to replace these three lines at the top of header.php in your theme:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" dir="ltr" lang="en-US">
<head profile="http://gmpg.org/xfn/11">
Fix that and then look at your
Markup Validation at W3C Markup Validator and see where the rest of the errors are. Once you have reasonably valid code, IE should display correctly....