One thing that I can't place though is the operation of the RAM-OS in your system. How has it worked for you? It has worked very nicely for me but if it made a difference for you then something else must be at work given the arrangement of your components, the supposed operation of the Intona and the reason for development of the RAM-OS being to reduce PC noise but reducing current draw in the PC.
I hesitate to jump into a thread where I am not very knowledgeable, but here's an observation/theory I've had about why the RAM-OS sounds so fantastic: when running the OS from RAM both electrical and vibration induced noise are eliminated. Prior to my RAM-OS I've had my spinning HD and fanless Seasonic PC power supply outside of the PC case on isolation footers. This step has always had a significant impact on SQ. When I first used the unplugged RAM-OS there was something very familiar with the sound that I believe has something to do with not having a spinning HD inside of the PC case. However, unplugging the RAM-OS went one step further to improve SQ because now electrical noise was also reduced. Today only my PC power supply is outside of the case and I make very specific adjustments to the sound with the type of footer underneath it.
One more observation: maybe it's my imagination, but try putting a 3.5 HD, or some other object weighing a couple of pounds, on top of your featherweight Intona. Seemed to solidify the sound a bit here.
Brian