Wide Area Bonjour not working

I'm not sure what you mean when you write "If I enable it the hostname no longer registers". Regardless, as support for WAB is limited and server side logs aren't available, it may be more effective to setup your own DNS server or find another service that offers better support for DNS Update (RFC 2136). Alternatively, you could use a packet sniffer to determine what updates are being sent, replicate those updates (and presumably failures or discrepancies) with nsupdate and then pass on your findings to support.

Generally, Dyn currently do not support automatic updates of IPv6 addresses (AAAA records). These are anyway almost static, so no need to update them automatically.

Also, did you read through this KB article?

Exactly Bonjour is about registring SERVICES, which do change, AAAA records need to be present to indicate the presence of the service.

Yes, I followed the directions in the KB article, that's how I got things setup in the first place. As for the IPv6 addresses not needing to be updated automatically, that's not entirely true anymore. First, Mac OS X 10.7 (maybe earlier versions) does try to create the AAAA record if IPv6 is on (and there's no way to disable it through the GUI). The AAAA record creation fails, preventing the A record from being created as well. Second, a lot of ISPs are planning on rolling out /64 IPv6 blocks to home users in the next year. I imagine these addresses will change as frequently as the IPv4 address changes.