Found this info in the CLP-area at http://www.lotus.com/
Here is why the agent bombs when scheduled even if ODBC is setup correctly on the server with a system DSN but the agent executes from the Notes client when run manually. When you are running the Notes Server as a service under NT it defaults to run as the "System". As such it has all rights afforded the NT operating system itself. When you run the agent manually from the Notes client it is executing under whatever account you logged into under NT (i.e. the GUI user). As with the server, the client has all access to resources as the user who is logged in. So, you log into the GUI as yourself with all access rights to whatever network resource where the database is housed, run the agent manually from the Notes client, and everything is wonderful. You then schedule the agent, it tries to access the resource as "System", and the process stops because "System" does not have access to the same network resources as your NT User Account. To prove this to yourself put the database in a local, unprotected subdirectory on the server (i.e. one that does not restrict use to certain accounts, particularly the local system) and see if the agent runs on schedule. Ours never had any problems running locally.
So, how do you "fix" this? Well the most simple way to do this is to have your Notes server service running as a user account. To change this, go into the Services Applet and double-click on the Lotus Domino Server service entry. You can then choose to have the service start under a specific user account by specifying a name and providing a password. Now for the bad news ... if you elect to run the service under a user account you will not see the console screen (i.e. DOS box) appear on your system when you log into the GUI. Why? The "Allow Service to Interact With Desktop" setting controls this and cannot be set when running a service under a specific user account. You will still be able to access the console through the remote console feature of the Administration Panel. I, personally do not like this because I have had instances where the server has been experiencing problems and could not be accessed through the remote console. I have spoken to representatives at Microsoft at length regarding this rights issue with no positive results.
If you have access to Novell servers, you have another recourse. Install and configure the GSNW (Gateway Services for NetWare). If the database is on the Novell server and the drive mapping is setup correctly you should be able to access the database using the scheduled agent. This is true even if you are running the Notes Server as a service. Why? Since GSNW runs at the system level, the "System" account has access to any of the drives mapped to the Novell servers and therefore the database. This is not without it's problems also. We have had some problems with "lost" drive mappings albeit not very frequently. Until the mappings are re-established the agent will fail. This has been our method of choice since it allows us to continue to use the server console and run the server as a service.
Of course one last option is to run the server software as an application under the GUI instead of a service. By doing so you get both the console and access to server resources available to whoever is logged into the GUI however you have the obstacles of how to insure that your server comes back up automatically if power is lost, etc.
In my opinion, none of these situations is ideal. Hopefully this will make the situation clearer and you can make a decision based on your company's individual needs.