Another KB article has been published for MSMQ over HTTP:
941754 Incoming messages may be rejected by the queue manager on the cluster after you configure the clustered instance of Message Queuing to use HTTP messaging in Windows Server 2008
The principle here is that MSMQ does a reverse lookup on the IP address to find the computer name - if the lookup fails then MSMQ isn't happy. This is similar to a previous blog where the lookup returned the wrong computer name from a HOSTS file.
I'm not sure how relevant it is to clustering and IPv6 - I suspect the problem is more generic than that - but I'll have to wait until I have some time to test it out.