Confounded by a problem with my Sony 5000ES receiver- please help!?

My Sony receiver is located behind some cabinets in my home theater system, controlled by a Logitech Harmony remote and a Niles IR extender system so I can control everything with the cabinets closed. I have both an IR flasher mounted to the front of the receiver and a plug going from the Niles unit into the back of the receiver. Everything works great unitl someone switches something physically on the receiver itself, then it ceases to respond to the commands from the IR repeater system for about a week or so, and then magically works again. It works fine directly from the remote if the cabinet door is open, but will not receive commands when the door is closed. This last time it has been out of commission for more than two weeks. I have young kids and leaving the cabinet open is not an option. I have tried combinations of the flasher, the control port, and both, and nothing works. Any other audio geeks out there that can give me some guidance on this?