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With output=xml, the validator is outputting a series of error <messages> but no <warnings> as it once used to. The offending code seems to be between lines 2136 and 2149, over here: http://dev.w3.org/cvsweb/validator/httpd/cgi-bin/check?annotate=1.432.2.2
This bug might be related to: http://www.w3.org/Bugs/Public/show_bug.cgi?id=1855
XML output is deprecated. Wontfix. http://validator.w3.org/docs/users.html#Output