Mark,
Our situations sound eerily similar. My engine is Windows 2003. We have a system (Datex Ohmeda, which is now part of GE) that is sending HL7 vital sign information to a port on my engine. It will work great for about 4 hours, then for no reason messages stop coming across. All I have to do is stop/start the inbound thread and everything is great until the next time. The inbound thread stays in the UP status and nothing looks out of the ordinary. Did you find a solution for your problem?
Ross