Wow, I'm sorry I let this sit in my inbox for so long. The fact that you see the incoming message in conversations yet you lack the notification makes this sounds like one of those mysterious corners of RTComm. The reason I say this is a plugin reports only new messages, RTComm stores them off. So since you see the messages in the history that would imply that TOR did send off a notification. I'm probably doing something slightly wrong in communicating with RTComm but with the closed parts and lack of Nokia support I'm not sure what next steps to take to resolve this.

I can at least take a shot in the dark and see if there is anything suspect in your log.