It seems that I was wrong. The issue does in fact stem from Coldfusion.
Since I did not create the page that was having the issue, I overlooked an important part. The person who created it was using the cfform input tags with verification. The caused Coldfusion to insert this into the rendered page at the end of the header:
<script type="text/javascript">
<!--
_CF_checkeditUserInfo = function(_CF_this)
{
//reset on submit
_CF_error_exists = false;
_CF_error_messages = new Array();
_CF_error_fields = new Object();
_CF_FirstErrorField = null;
//display error messages and return success
if( _CF_error_exists )
{
if( _CF_error_messages.length > 0 )
{
// show alert() message
_CF_onErrorAlert(_CF_error_messages);
// set focus to first form error, if the field supports js focus().
if( _CF_this[_CF_FirstErrorField].type == "text" )
{ _CF_this[_CF_FirstErrorField].focus(); }
}
return false;
}else {
return true;
}
}
//-->
</script>
Now I'm not entirely sure what this is doing to cause the meta tag to break, but when I remove the module that causes this script to be generated, the issue is fixed. When that is removed text compare shows that the rendered headers in both pages have 0 differences.
I completely fixed my specific issue by setting the WebConfig in IIS itself.