We recently moved to a three-node Exchange Server 2003 cluster with two active nodes and one passive node. Outgoing SMTP messages are marked with the IP address of the physical node from which they were sent instead of the cluster's IP address. Is there a way to change this behavior?

No. This is an artifact of the way that the Microsoft IIS SMTP service works on a cluster: Outbound messages appear to have been sent from the physical node. In most circumstances, this behavior doesn't cause any problems, but some firewalls and content-management tools have trouble with a single network resource that uses multiple IP addresses. If this is the situation you're in, you'll need to configure the firewall or tool to accept the additional source addresses.