Not sure if anyone can hear the difference, but I guess a not perfect SPDIF card may cause plenty of jitter: not-perfect clock, electrical jitter, electrical noise from computer power supply, other boards (they are not shielded, right?).
Noise from funs and hard drive causes you to choose between it (the noise) and long run of cables if you put the computer into a closet.
Plus, I doubt you have a software HDCD decoder :)