"I'm slightly confused. my domain is not a *.dnydns.org domain, it is a fully registered domain name."
If you're using dyndns.org for this, and trying to use the dyndns.org script, that's your problem. dyndns.org, for reasons known only to them, uses different service names for the *.dyndns.org domains than for the full domains.
This can be easily changed. Edit /sbin/e-smith/dynamic-dns/dyndns.org, and change line 20 to begin with
system=custom
instead of "system=dyndns". That should take care of the problem.