It sounds like you're not using a BOS right now, and a "standalone" Persistence Manager does not use WCF at all, so I'm not sure what your question is. If your service is not the BOS yet it's gone "mad" after a port, how can we help? If your service is the BOS or is talking to a BOS, then maybe we can help diagnose the problems you're seeing.
A "standalone" Persistence Manager - ie, a PM which does not communicate with a BOS, but instead directly accesses the database - does not use WCF. With one exception, if the CommunicationsTechnology setting in your ibconfig is "WCF" the trace file logging will use WCF for communications between the app and the tracing service. If this is causing problems, you can change the CommunicationsTechnology to the default of "Remoting".