OK...I uploaded two versions of your style (the original and edit). I then compared the VarStyles, Main CSS and Templates. I think I've managed to pinpoint the source of your misalignment.
In your navbar template find at the bottom:
Code:
<!-- USC header edit start -->
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
$usc_left
<td valign="top">
<!-- USC header edit end -->
When I removed this section of code the misalignment was no longer an issue.
I also removed in your footer template the ending code:
Code:
<!-- USC footer edit start -->
</td>
$usc_right
</tr>
</table>
<!-- USC footer edit end -->
I've tested this on both IE and FF browsers. Try the changes and see if you get your desired results. Let me know how it goes.