template_rdf() isn't working correctly. Line 242 in comment-template.php:
if (strpos($_SERVER['HTTP_USER_AGENT'], 'W3C_Validator') !== false) {
Replacing it with:
if (!stristr($_SERVER['HTTP_USER_AGENT'], 'W3C_Validator')) {
fixes the problem.
Basically it was working the the opposite of what was expected. The trackback code was appearing when trying to validating the page and wasn;t appearing otherwise.
Just for clarification, did you have the template tag, trackback_rdf, wrapped in an HTML comment as recommended ?
Now that you mention it, no (but I will do so, thanks). That would make no difference in what I saw, though.
Changing it to:
if (strpos($_SERVER['HTTP_USER_AGENT'], 'W3C_Validator') == false) {
Would be slightly faster, in theory.
Anyway, I put this bug into trac:
http://trac.wordpress.org/ticket/4390