Thanks for the reply. I was on the second to latest firmware when the problem started, and I have just recently updated. The problem existed under both firmware versions. Also, HDMI control is off. I've had the receiver since Aug 2010, with the same components hooked up, and this has never happened before. I'll try disconnecting the Onkyo ipod dock, and see what happens. I noticed that this only happens after a cold start. If I leave it on, it will work fine for hours, but audio will almost certainly fail if I leave the receiver on standby for a couple hours.
Does the 3008 have any kind of diagnostic menu? I wonder if it is sensing a short and going into some sort of safe mode.