Back around March/April, I had my TX-SR606 serviced by an authorized Onkyo service center, on Onkyo's dime. The tech told me he had replaced all the bad capacitors, but didn't state how many. Anyway, the OSD was finally working, but the HDMI issue (which was the main reason I took it in for servicing) persisted. When I called the service center back, the tech told me that there was nothing he could do to make HDMI devices connect quicker.
Fast forward to late September and the handshake issue has gotten worse. Now I had to warm up the amp for about 40 minutes before it would recognize any connected devices via HDMI. But it got worse, not only did I have to warm up the amp, but now I had to wait a couple more minutes for my devices to handshake properly!
So yesterday I decided to attempt to fix the handshake issue by replacing the rest of the caps. So what did I find when I opened the amp up? I found out that the #$%^$ service center did nothing but solder on 1 capacitor as a bridge between two chips! That's it! They did just enough to get the OSD working and nothing else.
Finally, this afternoon I replaced all five caps -- using the tutorial in this thread and Ed's Youtube video -- reconnected every thing and fired up my amp and PS3. Success!!!
Every thing is now working properly and it now only takes 3 seconds (like it should) for the amp to recognize my HDMI devices and the OSD still works!
I'd like to thank the OP for taking the time and sharing his knowledge, on how to fix this handshake issue, with the AVSforum community. I will also be filing a complaint with Onkyo about the service center.