Hmmm... This is one of those where you simply have to know how it works. On Windows 2003 Server, 64 bit version, there are two OBDC control panels. One for 32 bit data sources and one for 64 bit data sources. Lotus Domino, being a 32 bit application, should use the 32 bit data sources but for some reason that doesn't work. It also doesn't work to add the data source to the 64 bit data sources. The problem shows itself by popping a UI error message on the server. If this isn't enough the agent is also halted without any apparent indication on the server console.
The solution is to add the same data source in both the 32 bit and 64 bit data source control panels. Then it works. Wierd!