Hi Peter,
I have exactly the same issue [1], [2] and [3] that you have described. I bought a 3.1 system a week back and have been seeing these issues every now and then. I have no idea why it's happening. Please let me know if you figured out a solution.
My set up:
2 RP-440WF
1 RP-110WSW
1 RP-440WC
I have an optical cable connected from TV to HD control center. To see klipsch menu, I have connected a HDMI cable from out to TV In.