A user recently asked me why as a logged in user his website url isn't linked to when even his website is specified on his profile page, but it does work when he posts anonymously and includes the information there.
I did some digging and I couldn't find anyone else posting about this here so I quickly solved it, if anyone is curious here is my solution:
What was involved was a simple edit to the comment-functions.php on line 6 making the logged in $user_url a global (already done for $user_identity etc). Then in the comments.php template page for my theme I added that as a hidden input field for logged in users in the "if $User_ID" section, and so it goes into the comment like it does with an anonymous user.
<input type="hidden" name="url" value="<?php echo $user_url; ?>">
So it won’t work for historic comments but it should go for ongoing comments.
It would be nice if this bug was fixed for a future release so I don't lose my $user_url tweak on an upgrade, but whatever -- hope this helps someone out there.