It appears that early in the morning of the 16th of July a new domain was added to spore.org (bkrscm.org) and, presumeably, create-tinydns-data was run. However, when it was run all zone files in /etc/tinydns/root/ were built using clone's old IP address. This IP still exists in create-tinydns-data.bak so perhaps that was run inadvertently?
I re-ran the script and the zone files are now all showing the proper IP address (minus the custom zones which all appeared to be fine in the first place).
Things'll probably have to propagate again before all is working normally again. But at least now a dig on clone itself returns a correct IP for, say www.zoiks.com.