I think ToG CSS was programmed for a mildly stretchy design in supported browsers 980px in IE. This should fix it. I dunno where you got 1090 from but 980px was chosen to leave room for the padding, and the scrollbar on a 1024 browser.
#mainInner {
margin:auto;
/*
min-width:230px;
max-width:1111px;
*/
width:980px;
background:#FFF;
border:1px solid #004480;
}
With this fix you can remove:
<!--[if lte IE 6]><style type="text/css">#mainInner{width:980px}</style><![endif]-->
However I wouldn't bother, doesn't make a difference.