The receiving site is supposed to respond with a specific piece of XML. Geeklog will then parse that XML and try to figure out if the Trackback was sent successfully or not.
If you get "Response not understood", then whatever the other site sent back either wasn't XML at all or it did at least not contain an <error> tag.
So Geeklog doesn't know what to make of the response. It is therefore possible that the other site received the Trackback just fine (as seems to have happened in your case). Geeklog just couldn't tell what happened from the response.
If you want to debug things, find this piece of code in system/lib-trackback.php:
Text Formatted Code
fclose($sock);
// firing up the XML parser for this would be overkill ...
$r1 = strpos ($res, '<error>');
The next time you get a "response not understood", check your error.log and see what the other site really sent back.
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<?xml version="1.0" encoding="utf-8"?>
<response>
<error>0</error>
</response>