I have an newer Onkyo Receiver and I do not have the problem you have, but I notice my Receiver does take time to turn everything on. I use a Harmony One, so everything turns on at once (not sure the exact order).
What I do see is that the Receiver seems to turn on first, and when the STB turns on it automatically reconnects, then when the TV turns on the Receiver does another handshake. What I see is a blank screen, I hear the audio come on, it goes off, then back on again with picture. All this takes a few seconds and coincides with the Harmony One turning on everything. The Onkyo seems to detecting each device and re-handshaking automatically to ensure it is connected correctly.
It appears to work as in should.
If you are using a Harmony, try turning on the devices in the following order
TV, STB, Receiver.
hope this helps