Your skin is using Solpart Menu it seems.
That's the old default Dotnetnuke menu and it's not developed any more.
It used browser specific rendering which is why it has issues with the new IE version.
The new default menu is the DDR menu.

There are two ways to solve this:
A. Use the new DDR menu's Solpart replacement.
For this you need to upgrade to DNN  5+ and...

Edit your skin's ASCX files, replace

<%@ Register TagPrefix="dnn" TagName="..." src="~/Admin/Skins/SolPartMenu.ascx" %>

with

<%@ Register TagPrefix="dnn" TagName="..." src="~/DesktopModules/DDRMenu/SolPartMenu.ascx" %>

B. Use a cleaner version of DDR menu and create you CSS from scratch.
http://www.dotnetnuke.com/Resources/W...

 HTH

---

     <script runat="server">
 Protected Sub Page_PreRender(ByVal sender As Object, ByVal e As System.EventArgs) Handles Me.PreRender
        Dim meta As Literal = New Literal()
        meta.Text = "<meta http-equiv=""X-UA-Compatible"" content=""IE=EmulateIE8"" />"
        Me.Page.Header.Controls.AddAt(1, meta)    
    End Sub
 </script>