Have you performed the latest firmware update for your Onkyo* receiver? http://www.intl.onkyo.com/support/firmware/tx-nr609.html
There is mention in the latest update notes of improving HDMI-Through functionality which may improve your issue. Additionally, when you are in the Intel® GMCP - what options, if any, do you get when you select the Onkyo* receiver from the dropdown?
I actually forgot to reply, but I figured it out. There's some picture setting on the TV called "dot for dot" or "dot to dot" or something like that. It didn't change the TV/DVD/Blu-Ray/gaming image at all (for better or worse, which is good), but for some reason it made the PC input fit perfectly on the screen as it should. So I just left the TV on that setting...
...Thanks for the reply!