How do I get Windows Domain Controller and Ubuntu dnsmasq to play nicely?

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http://serverfault.com – I've inherited "ownership" of a network which has a Windows 2003 Server running as a Domain Controller and file server (no IIS or DNS running). We also use an Ubuntu server running dnsmasq as an internal Name Server. This setup doesn't seem to have been a problem until now - we are installing a new Windows 2008 server (new hardware and everything), and want to migrate services and data from the old server gradually. To start this process, we are trying to add the new server as a secondary controller on our domain. The server is connecting to the domain easily enough, but when we try and speci (HowTos)