Well I did the system reset then re-calibrated it using the setup mic and it's still doing it. It seemed like it was doing ok switching to the PS3 a couple times but the audio was still lagging and when I went to switch back to my satellite receiver my tv blinked "waiting for signal" like 5 times before the picture actually came up. If there's no signal at all the message just stays constant so the fact that it was blinking tells me the receiver was trying to connect to it and failing...
My problem is that none of these things make it unusable, so if I take it back to get worked on again am I going to just seem like an anal jerk?
What you are getting now is within the bounds of normal for HDMI/HDCP hand shakes, unfortunately. I have no idea why this board is slower then the last. May be these were a problem board, and there has been some redesign, which has caused the delay you have not had before.
All I can suggest is that you contact Onkyo and ask what is a normal response time for a hand shake with this unit when changing sources.
The other issue is that you can not rely on satellite/cable boxes as a valid criteria of correct working in this regard. These companies do not pay for HDCP certification, and most of them have HDCP code errors. Some of these errors are so severe that some cable boxes will not make a hand shake at all to certified devices, like your receiver. So it could be your new board has the latest HDCP codes and your satellite box is rogue to some degree.
If this only happens with uncertified devices like you satellite box and not with certified devices, then that is your answer.