Continuing testing.
Connected rfx9400 in network mode. Measured output voltage to be the same as the rfx9400, between 2 and 3 volts. Connected to ZR-6 and it worked.
Connected rfx9600 again and measured voltage to be between 2 and 3 volts. Tested again and it worked. Why? Very odd, this has never worked in the past.

What was different this time? Well, I removed the ZR-6 and rfx9600 from my rack to move into the room where I had an IR repeater system set up for testing.

I moved the ZR-6 and rfx9600 back to the rack and reconnected everything.
Tested again and the global IR would no longer work. Hmmm. Okay, has to be something connected in the rack that was not connected when it was out of the rack. (Remember, I had the same problem at my customers house with his ZR-6 not accepting codes from the Global IR input and I changed his configuration over to RS-232 to resolve the issue.)
I disconnected the RG6 from the FM antenna input and tried again. IT WORKS! Connected antenna back up and it stopped working again.

I tested both the codes from the O1R1 database and the ones Niles tech support sent me. They both work as long as the antenna is disconnected.

Has anyone seen this? My antenna is a simple antenna coming from my attic, but is split off about 8 times for ATSC tuners throughout my house. Mostly Tivo Series 3 boxes. I have no in-line amplifier of any kind. My customer has a dedicated antenna, but it is amplified because he lives way out in the country.

Ideas?