Your problem is not handshake. It's the HDMI ports on the Onkyo. I purchased an Onkyo TX-SR707 in Nov 2009. My Sat box was cutting out every few seconds. I communicated with Onkyo support who told me to reset the unit every time i contacted them. This btw didn't work.
I then tried every HDMI port on the unit and actually found one that works flawlessly - the DVD/BD (HDMI 1). I had to then go through the same process with our PS3 and it finally worked on the CBL/SAT (HDMI 3) input. Also, i bumped the Sat box down to 480p and it worked fine on all ports. HMMMM. Onkyo now tells me i have to bring it in for repair. They won't replace it and since they didn't even attempt to "troubleshoot" the problem, i missed the 30 day exchange window.
i have not yet had the unit repaired but have read several posts about HDMI daughter board failures.