You mentioned that the agent is signed with a Lotus Notes ID that the Domino server allows to run agents -- that is good. The other part is a setting that I believe was new in Lotus Notes Domino R6 that allows Lotus Notes databases on one server to open databases on another server in the background. Prior to Lotus Notes Domino R6, there was no protocol in place to allow that trust.
In either Lotus Notes Domino R6 or R7, you need to open the server document of the Lotus Domino server that contains the target database and add the name of the server containing the Web service to the "Trusted Servers" field on the "Security" tab.
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