I did some more tinkering with my setup and the Yammy tonight.
Adam, you were right, I can do all my own bass management in Windows and I get some nicely balanced sound out of it. There is a checkbox in Creative's own software that says "Subwoofer Gain": when disabled, I have virtually no subwoofer, and when enabled, it's a-okay. Quite nice, actually. I could get used to it.
In Ubuntu, no such option exists, but I have found a sound management software that gives me independent volume sliders for each channel. It's a bit buggy, as in it keeps forgetting settings periodically and the sub ends up switching to standby. However, it does allow me to apply a 11 dB boost to the LFE channel.
Even with that, the sub doesn't sound anywhere near as good as when I play back in Windows or pop a SACD into the Oppo. I tried the same titles from my PC and then from the Oppo.
Here's what I'm wondering: could the RX-V661 have the LFE bug?!
If I understand correctly, my sound card passes the analog sound to the receiver as PCM. So if Linux's available software doesn't do the subwoofer gain, then the receiver gets an un-amplified signal and due to the LFE bug, the sub sounds weak. Could that be what's happening? Cos the Samsung clearly sounds way better, I tried again tonight.
I have set the Oppo to send the sound out as DSD, but when I set it to PCM, it sounds fine as well. That may be because the Oppo has its own bass management, no?
My Nvidia graphics card has its own Mini-HDMI out, which should be able to play back sound. Unfortunately, it doesn't. I tried both in Ubuntu and Windows, and it stays silent on both.
Riddles, wonders... :-/