You probably want to change !(IE) to (!IE)
Also, the "normal" <body> tag you're talking about is in a conditional comment. The fact that it's on a different line doesn't matter, it's still inside the conditional comment tag, so is affected as such.
Conditional comments for IE work by using normal HTML comments <!-- --> so any code inside a "false" conditional is just commented out; <!-- <body class="ie6"> --> IE then has its own syntax inside of that. As such, non-IE browsers just see a commented string, and IE treats it as a statement to execute.
Because of this, only one body tag shows, and only that one gets used.
More explanation of
<!--[if (gt IE 9)|!(IE)]><!-->
<body>
<!--<![endif]-->
To IE, this says:
<if greater than ie9, or not ie> (ie conditional comment)
<!--> (empty comment) (--> putting this here to stop SO ruining syntax highlighting :D)
<body>
<end if> (ie conditional comment)
If you don't understand why, read the paragraph starting "Conditional comments for IE work...".
This same block, to any other browser looks like this:
<!--[if (gt IE 9)|!(IE)]><!--> (this is just one comment, containing the text "[if (gt IE 9)|!(IE)]><!")
<body>
<!--<![endif]--> (again, just one comment, containing "<![endif]")
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