I've had a problem for a long time with my 622 connected to my Onkyo TX-SR606 by an optical cable. Once in a while, when I turn everything on, the only sound I get will be from the subwoofer. I can usually fix it by changing the channel up or down, but sometimes that doesn't work because the channel I change to is also using 5.1 (it only happens on 5.1 channels) so rather than wasting time scrolling up or down to a channel that isn't 5.1, I toggle the power on the Onkyo.
I can't imagine what the problem is, because both optical audio and component video are one-way connections, it's not like there's a HDMI handshake issue going on. I always assumed that the problem must be with the Onkyo, but, I can't imagine why it wouldn't just keep trying to recognize the signal til it got more than one channel, so I really don't know.