The examples tool does not hand configs for Windows2003. I assumed (incorrectly) that the config would either match the listed 2000 or XP config. I was wrong.
I got the 2003 machine working as a tunnel endpoint using a slightly altered version of the XP example. Specifically,
netsh interface ipv6 set teredo disabled
netsh interface ipv6 add v6v4tunnel IP6Tunnel $CLIENT_V4_ADDRESS $SERVER_V4_ADDRESS
netsh interface ipv6 add address IP6Tunnel $CLIENT_V6_ADDRESS
netsh interface ipv6 add route ::/0 IP6Tunnel $SERVER_V6_ADDRESS