Using WordPress 1.5.1.2 for testing purposes I discovered that outgoing trackbacks are not correctly handled by the XML-RPC interface. I'm using MarsEdit to edit my posts.
MarsEdit sends its list of trackback URIs as an array following the form:
<value>
<array>
<data>
<value><string>http://my.trackback.url</string></value>
</data>
</array>
</value>
Now WordPress seems to expect a comma-separated list of URIs. I don't know which one is the preferred behaviour here, but I do know that WordPress does only save a string named "Array" as a single URI. This happens, when I add new and edit existing posts (mw_newPost() and mw_editPost() in xmlrpc.php).
The second issue is that when editing a post (method mw_editPost() in xmlrpc.php), the ID gets lost. It magically reverts back to 1 during the update (line 617 in xmlrpc.php), but is still used for sending out trackback URIs later on.