Dear Tom,
I have started my quest for the holy grail of htpc 2 years ago and have found it about a month ago. I set for myself the following requirements:
-it must be 1 box that is able to handle ALL available media
-it must be user friendly and relative dummy proof: no switching audio formats and settings in between movies, just press play and experience the magic (a typical non-tech minded person must be able to play it all)
-it must serve as TV-VCR in it's highest possible quality
-the audio quality must be at high end hifi quality in such a degree that if you play FLAC from it professional hifi dealers are blown away
-video must be full-HD
-it must be able to play current videogames fluent in full-hd res
-it must be able to handle all bluray audioformats flawlessly including dts-hd, master and LPCM WITHOUT HAVING TO SET ANYTHING OR SWITCH ANYTHING in the settings of the htpc
-it must appear and look like a receiver, not like a pc in the living room
-the surround sound must meet THX reference standards and volume
my quest led me through (funny) the exact same products and their respective problems among many others. I was able just like you to get the digital passthrough to work with the Xonar 1.3 deluxe but with that card a few problems remain such as having to switch standards before playing it in the Xonar console, malformed LPCM that sounds flattened and lacking bass etc and last but not least the very slow hdmi-video switching of all Onkyo receivers so that wasn't perfect. Then I went to a hi end hifi seminar and listened to the professional audiocard of Onkyo and was totally blown away by the amazing crystal clear sound quality it produces in combination with a proper receiver that amplifies the channels seperately in a fully analogue way. That's when the light hit me. I rebuilt my entire htpc concept around this "analogue" setup and left the trail of the "immature hdmi" path. The result was amazing. 1 time calibration with the aid of Vista Ultimate built-in room correction and I was in the middle of the best htpc experience I had ever witnessed. I'm so happy with the result since it meets all the criteria of the holy grail. I also store and stream bluray content in full size on a 6.5TB windows drive at the speed of full gigabit (RAID 8*1TB) and play it with Arcsoft TMT 3. High dev TV functionality is provided with Firedtv, an austrian solution that allows digital satellite HD streams to be displayed directly on the pc with a modified version of DVB viewer as software (more userfriendly). For the analog amplification And all that in a fusion remote case from Antec é voila, there's your holy grail in a slim slick box