[[Note: While this problem has been caused by a plugin, I do believe that it is a WordPress issue.]]
Currently, WordPress seems to confirm pingbacks using a blank user-agent. This is a common technique used by spammers to avoid spam filters, and as such, it is now blocked by Michael Hampton's "Bad Behavior" v1.2.2. Any attempt to send a pingback while using Bad Behavior v1.2.2 will fail, because the confirmation request from the pinged blog will be blocked for having no user-agent. While this problem has been caused by a plugin, I do believe that it is a WordPress issue. WordPress should not be using common spamming techniques. And, after all, why not identify WordPress' confirmation requests with a user-agent like "WordPress"?
Michael Hampton's "Bad Behavior" can be found here: http://www.ioerror.us/software/bad-behavior/