I hope you are right. I should add that I when I listen using headphones the missing element is back even though it is fed via toslink cable. My comment is strictly in a direct to amp set up with optical out. The texture, space, and weight sound right through the heeadphones.
3/31/13 I need to ad an ademdum: Today I moved the computer and TV cable box further away from the Nuforce DAC and Marantz power amp. It sounds much better. The problem might have been EMI/RFI interference.
Interesting. I don't normally think of that as being a major contributor to the sound, but of course it is a possibility. And in your case maybe that's exactly what was at play. Good thinking as far as moving those boxes away. A USB to SPDIF converter could still bring even more improvements, but at least you got rid of your main complaint.