As to the problem with the track back link, don't use it I found it confusing as well because it gives the pingback address not the track back address. in other words it takes you to the permalink. I replaced the code in my comments and popup comments to display the address in text form. here is the code from my comments.php for rss and trackback.
<p><?php comments_rss_link(__('<abbr title="Really Simple Syndication">RSS</abbr> feed for comments on this post.')); ?></p>
<?php if ( pings_open() ) : ?>
<?php _e("The <acronym title=\"Uniform Resource Identifier\">URI</acronym> to TrackBack this entry is:"); ?> <em><?php trackback_url() ?></em>
<?php endif; ?>
give it a try.
For the confusion on trackback and pingback:
pingback is the link you embed or use in your post. this will be done automatically if you have it enabled. It can also slow down your publishing if there are allot of links to check.
Trackback is the link you put in the trackback box.
Both send information back to the site you are linking too. Mine uses a brief summary.
I have gotten everything except send trackback to function.