I like the idea of diode isolating the various sources.

Does the RFX9600 work if it is the only source on Input Zone 1? Have you tried using another RFX9600 output port? For the first test you don't need to reprogram anything, simply check to see if the network goes down.

IR emitters are a simple LED, usually with a series resistor. When connected to the diode tester you will have conductivity in one direction, but not in the other direction. The testers usually indicate a voltage in the conducting direction. The voltage indication should be similar for all of the emitters.

It would be great to monitor the ZC21's inputs with an oscilloscope. You could monitor the inputs with a multi-meter, but it is difficult to predict exactly what you will read. Check both DC and AC voltages and compare readings for the various sources while sending the same IR code. I don't recall offhand exactly what the output of the various sources. Probably a logic '1' is +12V. If the voltage collapses or goes to a rail when the RFX9600 is connected, that's a strong hint that there is an issue with the RFX9600.