Bwah, apparently they changed some of the functions relating to all of this between 2.1.2 and 2.1.3, which caused me a bit of confusion when looking at different versions of source code.
The clean_url function looks like it has some semi-important stuff in it, so I was hesitant to comment the whole line out, so I took a closer look and narrowed it down to the following change:
wp-includes/formatting.php @ Line 1082
$protocols = array('http', 'https', 'ftp', 'ftps', 'mailto', 'news', 'irc', 'gopher', 'nntp', 'feed', 'telnet');
$protocols = array('http', 'https', 'ftp', 'ftps', 'mailto', 'news', 'irc', 'gopher', 'nntp', 'feed', 'telnet', 'ventrilo');
Thanks for your reply; it definitely pointed me in the right direction. It's a shame this turned out to be a core file edit. That always leave a dirty taste in my mouth.