I agree that the problem is almost certainly noise. Way back when, I could tell which way my floppy drive was seeking based on the direction (dexter/sinister) of the diagonal noise bands on my TV, 10 feet away. Things are quieter now, but noise is not gone. More CPU activity will cause more transistor switching and a non-zero noise increase. The motor and voice coil in the additional drive generate noise, too. And noise on the power rails will certainly affect the linearity of the DAC. Jitter shouldn't be an issue due to (as mentioned before) data buffering. However it is not impossible that noise could affect the clocking of the data samples into the DAC. It's also (barely) possible that extry heat could be affecting things. But the delta T is so small. But I just replaced the fan on my graphics card. It lowered the temp ~10-20 C. And now there's no more texture shimmering. However, this is orders of magnitude more heat. Most of these things are very to extremely low level. But audio is an odd beast. As are head-fiers
In the box noise is used as a selling point for external sound devices, but we all know how advertising works.
Two fairly conclusive experiments suggest themselves to me:
1) Use an external USB DAC. I have a cheap Turtle Beach Audio Advantage that I would be willing to loan out (if I can find it) since I'm very curious about what's happening. I don't know if its SQ will be good enough to show any differences.
2) The *real* test would be sending WAV and FLAC to a high end DAC & HP amp system using the card's digital out (if present) or bypassing the card entirely using a USB DAC or USB -> S/PDIF -> DAC. The TB AA does USB -> S/PDIF optical conversion. I don't know if it's bit perfect, tho. What are some some songs you listen to that really show the differences? I'm curious to see if I can hear anything.
A quick thing to try would be to see if your mvsik player can convert FLAC to WAV and write it back to a file. Then do a comparison. You could be experiencing an encode or decode bug.
Sorry if this has already been suggested, but 11 pages of posts is a bit much to wade thru.
(the long winded)