Well things seem to be moving along apace...
The desktop, laptop and the other laptop used in the tests I mentioned earlier which failed to replicate the issue were all multi-core machines for everyday use, running XP, 7 and 7 respectively.
The USB receiver Stan uses is the PCM2902 according to the website for TC-7520 if that makes any difference.
Stan, can you recollect the equipment used and how it was coupled when you noted these differences? I presume you used your own DAC when you discovered this?
It may or may not be related, but it may help flesh out the circumstance to further isolate the cause.

One other thing I forgot to mention (reported previously on issues over async b adaptive v spdif) for fullness was that we also connected my dac on usb to the optical input on my pal's DAC to see if that made any difference in the test, there was also no change in terms of the FLAC/WAV issue. There was however a qualitative difference for the better over the direct optical to his DAC which we both found surprising from a cheap chinese async DAC.

Could the issue really be as complex as the combination of player, processor and DAC implementation, perhaps even the OS?
If it helps, I can give a full rundown on my desktop and laptop where the problems do not arise?