very long pretty indepth post
Heheh, I know what you're getting at, unfortunately my original explanation perhaps isn't the clearest.
Unfortunately the full RGB crush is an issue Yamaha haven't fixed, saying they can't fix it as it's hardware...yet strangely they fixed it in the higher end version of the box. There have been major discussions over at AVS about writing a custom firmware; or trying to persuade Yamaha to correct the issue; but so far Yammy's head has been in the sand on the issue.
I actually have all my other equipment set to limited rather full RGB, and to be honest, in my opinion they all look really good, very natural, and the blacks don't bother me as in comparison to anything I've used previously, I just found for 'whatever' reason, the PC seemed to be slightly paler in it's blacks; and changing to component fixed that for me, probably because I use a lot of blacks on the pc; now this MAY be an intricacy of the amp vs the HDMI ATI setup and less restriction being placed on component feeds, however I do get what you're saying, ideally I'd have everything calibrated to high hell, but given the recommended settings already look brilliant for my HDDVD/PS3/Xbox it seems a shame to change the universal settings to suit the PC more; whereas changing to component output from my PC dealt with that issue.
As I say this may well be an intricacy of the combination of my AVR, TV and the ATI output, because when set to default limited RGB in CCC, whilst the computer loads from bios, before it hits Vista, the blacks are actually blacker (identical in my eyes to the component output setting). When this switches to windows and the ATI drivers/settings load, and the switch is made to default RGB output over HDMI; the blacks lose that inkyness slightly, reverting to the slightly greyer blacks.
Sorry its a little hard to explain without sounding like an idiot, but this is part of what makes me believe it is something particular with the setup, as everything else looks fine, and are as far as I remember set to limited RGB where controllable due to the amps inability to pass full RGB, and instead cutoff the WTW and BTB parts of a full RGB signal (NOT GOOD!)
Last Samurai (HDDVD), Transformers (HDDVD) Dark Knight, Xmen 3 and Wall-E look stunning via the respective players.
Out of interest what settings do you use; I'd be interested in trying them!