Just for the record, we found the issue. There was some filtering
being applied in the bridge code which randomly (?) dropped some DNS
requests. Setting:
net.bridge.bridge-nf-call-arptables = 0
net.bridge.bridge-nf-call-iptables = 0
net.bridge.bridge-nf-call-ip6tables = 0

completely resolved the problem.

I've written up full details here:
http://buriedlede.blogspot.com/2012/07/debugging-networking-problems-with.html
 -nld

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