I set it up this was to remove the AVR from the chain for my wife's benefit. My wife doesn't get along and play well with technology. Having things setup in this fashion, she hits one button and everything works just dandy; the TV and Cable Box power on. She can listen to the television via the television speakers or with a set of headphones and doesn't have to worry about switching errors. Remembering switching reduces her to tears. A man's toys are not meant to cause one's wife to cry in frustration. Hence the need to keep things as user friendly as possible. One button access, equals no tears and with the cable box provided premium channels, she has all the movies she can digest with no need for the AVR.
We have two cables going into the television. One for the cable box and one from the AVR. When the Blu-ray player is used, the Blu-ray information is auto passed (switched) to the television via the AVR. My wife has no need to even look at the AVR when used in this fashion.
The third HDMI cable goes from the Blu-ray player to the AVR.
As to HDMI cables, one needs to be sure to have "High Speed" HDMI cables. I've read that a lot of intermittent problems are cured by replacing HDMI cables with High Speed HDMI cables. Don't know if that will be your case but if your cables are not High Speed, I would encourage having your cables replaced to see if doing so solves the problems. MonoPrice has a boatload of well priced, High Speed choices.