My 606 does this... but I know why.
I recently changed my TV to Panny P42V10 and all of a sudden my 606 would start changing inputs on it own.
It would appear that this is viera link in action that is changing the inputs on the 606.
So by adding a viera link enabled TV all of a sudden there is communication between the tv, the amp and the blu-ray and they all think they know best.
My 606 does this it is when there is nothing on any of the inputs and its hunting for one.
As the TV is hooked up via hdmi it is actually supplying a signal back via the HDMI to the 606 this really gets it in a tizz.
On my 606 in the HDMI settings is the onkyo equivalent of viera link ,Control, Power Control and TV Control.
Try disabling these or similar options.
Certainly disabling HDMI Control on the onkyo might prevent it.