Hi SSwain
I have come across this problem too with a different model Onkyo receiver when used with other items such as blu ray player and you use the receiver as a switching unit. Onkyo were top dog and were on the case straight away and were aware of the problem and certain ways of curing it. We had a Onkyo TX-SR507 amplifier (new model) hooked upto a Panasonic TX-P42V10 (new model) and this had handshaking issue's also. There were 2 ways to solve this, step 1 was to send it to Onkyo to get it updated, which maybe would of took some time, step 2 was that Panasonic them self issued a firmware update to update the tv itself as they found this would be a quicker way to solve the problem, they are a big company and have people on the ball making updates regulary, so this is what ended up happening, Panasonic sorted the problem out in conjunction with Onkyo and bobs your uncle, it was up and running.
So in answer to your question, yes its a common issue with HDMI handshaking as Onkyo's products are great but its very hard for them to know how each manufacturer's HDMI will respond, hence this issue, so i think you will either need to contact Onkyo directly and see if they have a fix for this (you will need to quote your make and model of tv as they are so precise with sorting these problems out) or you contact Sony to see if they have a fix for this. If Panasonic issued a fix for their tv's to work with Onkyo receivers, i should not see why Sony cant do the same.
I hope this helps.
Regards> M
Panasonic Store, part of the Panasonic retail partner group
Panasonic TX-P46Z1, Pioneer BDP-LX52, Yamaha YSP1100, Humax FoxsatHDR, B&W ASW610, Clearer Audio Copper Line, Van Den Hull Flat, TCI Coral, Russ Andrews The Mains Block and Classic PowerKord.