I'm aware that this post is slightly on the old side, but since I'm using a similar setup, in that I'm running Windows 7, XBMC connected up via my Onkyo 609.
I initially had issues with Windows completely forgetting my settings when I put my amp in to standby so outside of XBMC when playing music for example sounded pretty hideous!. I re-installed the audio driver and that resolved that problem. I don't appear to have any re-negotiation issues when I bring my amp out of standby, audio will always come back.
Are there any extra HDMI settings you might be overlooking on your amp?