A few weeks ago, I wrote Onkyo support with this....
tl;dr unit clicks when breaks in digital stream.
I have a NR5007 receiver and love it, except for when there's a break in the digital stream and the receiver clicks. This happens when I pause my DVR as well. The DVR is hooked up via HDMI to the receiver. If I disable the subwoofer, all is well and there are no more clicks...however, I then have no subwoofer. Another example is that if the stream is lost or corrupt, it seems like the relay will go wild and you will hear it for about 3 seconds quickly clicking away. Please update the firmware so the subwoofer relay does not click if the digital stream is lost. I'm a reader on the avsforum.com web site and there are LOTS of people with the same issue and request. I can understand if you're going from one surround sound to another, or 5.1 to 2.0, but I'm not. Please update the firmware and provide a fix!! It would be great if the sw relay wouldn't turn off, or if there was at least a 30 second delay before the circuit was relayed off. Thanks!
They said take it to a support center for firmware updates. I asked if the firmware updates are the same you download on the internet or apply with a sub stick, and they said that the usb and internet updates are the same.
I was wondering, does the service centers have additional firmware updates or hardware modifications to fix the clicks?