Layout problems/Strange theme behaviour with IE6/'Show template filenames in HTML comments' set to On

It seems that with with 'Show template filenames in HTML comments' set to On
layout will not appear as expected in IE6. Other DOM user agents such as
Mozilla and Opera do not appear to exhibit this problem.

When 'Show template filenames in HTML comments' is set to On html comments
obviously appear in the markup showing template filenames that have been
used to produce the content. The first comment will appear before the
<!DOCTYPE... tag. It seems that with the comment present IE6 will not see
the document type/DTD information and so not use standards compliant mode.
This will cause your layout to not appear as expected.

- The recommendation for the document type object is as the first child node
of the root document node. As it is a recommendation this issue is not IMO a
bug with Xaraya but a(nother) feature of IE6.

More information on IE6 document types can be found here (though not on the
behaviour described above):
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnie60/html/cssenhancements.asp