You need to put a space for the <!-- [if !IE] -->
My full css block goes as follows, since IE8 is terrible with media queries
<!-- IE 8 or below -->
<!--[if lt IE 9]>
<link rel="stylesheet" type="text/css" href="/Resources/css/master1300.css" />
<![endif]-->
<!-- IE 9 or above -->
<!--[if gte IE 9]>
<link rel="stylesheet" type="text/css" media="(max-width: 100000px) and (min-width:481px)"
href="/Resources/css/master1300.css" />
<link rel="stylesheet" type="text/css" media="(max-width: 480px)"
href="/Resources/css/master480.css" />
<![endif]-->
<!-- Not IE -->
<!-- [if !IE] -->
<link rel="stylesheet" type="text/css" media="(max-width: 100000px) and (min-width:481px)"
href="/Resources/css/master1300.css" />
<link rel="stylesheet" type="text/css" media="(max-width: 480px)"
href="/Resources/css/master480.css" />
<!-- [endif] -->