I would assume the configuration is not correct in one of two places. One is the Domino Server configuration. Specifically, the naming and/or the routing of the TCP/IP requests based on the Domino Server name. The Redbook for configuring the Domino server and the E-Mail framework will help. Pay close attention to Chapter 2, which contains a general TCP/IP configuration scenario for the AS/400 and the Domino Server Naming section.
The other area is the SMTP setup in distribution. If you are using SMTP (POP), you must configure your distribution queues and TCP/IP routing, along with the directory entry, to point to the correct e-mail server (WRKDIRE). The other resource I would recommend is IBM's Lotus Domino site, which should contain all the information you need to find the problem.
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