Re: How can I set it so that the DOCTYPE is left as it is in the .ss file?
IE expects that the *first* line is the Doctype. You have probably the "<?xml version="1.0" encoding="UTF-8"?>" tag there.
This tag is unnecessary if you make sure the server delivers utf-8 per default.
You can do that via php:
header("Content-Type: text/html; charset=utf-8");
...or .htaccess:
AddDefaultCharset utf-8
... or html:
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
</head>
Edit: Silverstripe already sends a proper utf-8 content-type per default. So just delete the "<?xml version="1.0" encoding="UTF-8"?>" tag or whatever you have there in the first line and IE will stop replacing the doctype.