As a DHC-9.9 owner who has been driven slightly nuts by this same problem for the 9 months+ I've owned the unit, I just want to share my findings. In all honesty, the problem is NOT that bad, and I would not let that keep you from buying one of these units, but Onkyo/Integra should find a way to correct this issue.
What happens is the moment you:
1) change TV channels
2) skip to the next track on a CD/DVD/blu-ray
3) or do anything that interupts the audio signal to the pre-pro,
the pre-pro senses a loss of audio signal. Once the channel change, chapter-skip or whatever is completed and the audio signal is restored, the unit picks up the signal again and starts outputting sound. The problem is, it takes the unit almost a full second to lock onto the audio signal again and output sound. So the sound comes back on abruptly, resulting in the "click" that people are reporting. It sounds like a relay switch of some kind.
I have yet to find a way around this issue, and notice it on ANY action that interupts the audio signal.
I have set a default processing mode for each type of audio signal (2 ch digital, DTS-HD, Dolby True HD, etc) and it does not eliminate the clicking. Maybe setting the SAME mode for all signals might do the trick, but I don't want to do that.
I would think that an easy solution for this would be for Integra to just put 1 second delay (maybe even .5 second) on the circuit that senses the audio signal. That way the unit wouldn't constantly think that the audio signal was cut off.