Hey Cucore,
To be of any real help, I'd like to know what's in the guts of your HTPC. Are you using a Motherboard with integrated HDMI audio AND Video or are you using a separate video card with HDMI audio support? Some model numbers would be really helpful. I've been working on my own HTPC at home quite a bit lately and have had to tackle some issues over the last couple of months.
As for the Onkyo's HDMI inputs: The first thing you should check (provided you haven't already, of course) is that you have assigned your HDMI input ports to specific input selections. For instance: DVD will almost always have HDMI 1 assigned to it. I generally assign HDMI 2 to Video 1 and HDMI 3 to Video 2, but you can do it any way that you like. Once assigned, I might change the inputs name from "Video 1" to "HTPC" or "Xbox 360" etc.
To the best of my knowledge the 806 provides very little feedback information to the source device short of letting it know that it is active and turned on. I do not belive it is possible for your 806 to recognize anything specific about your HTPC rig. All you should need to do is ensure that you are sending it a video signal and a bitstream audio signal. If your HDMI audio driver doesn't support bitstream audio, then it should be converting everything to PCM.
It's been a couple of months since I really dug into the latest gear available for HTPC builders, but if memory serves having audio go out over the same HDMI cable as the video is a pretty new trick. Previously, it was necessary to have a separate digital audio output to get your audio. It's entirely possible you have some new gear- hence my question about the model numbers etc...
Looking forward to hearing back!
Caleb
Caleb Denison
Home Theater Guru
Aperionaudio.com