My experience was the mirror image of the OP. I had a Wadia transport running coax to a Benchmark DAC. When I ripped the CD's to FLAC using JRiver, then to the same DAC using Wireworld Starlight, things sounded noticeably better. Maybe some DACs do USB better/worse than other inputs. There are some optimizations for JRiver, easily found with Google. I'm running the tracks out of memory.
USB SQ, what can one expect
Have been trying out the USB connection on a Resolution Audio Cantata. The wire I've been using is generic (nothing fancy)and I've been using a Dell laptop using JRiver just to try this out. My problem is that my CD's played on the transport built into the Cantata just sound fantastic, three dimensional, everything and the same CD's ripped to the computer don't hold a candle to it played over the USB. I've also tried some high rez downloads. Is this to be expected or is the problem that I need to optimize the USB playback more. Thanks for any guidance that can be offered.