It very well could be, Shadorne. I don't know...I can only tell you what I hear.
And I don't doubt you. Here is a manufacturer's explanation for why differences are sometimes apparent when "in theory" there should be NO difference.
It turns out that most software is sadly lacking and sloppily made (but if you use anything made by Bill Gates then you won't be surprised at all -surely you will have noticed obvious deficiencies/glitches on a regular basis, so it should really come as no surprise that bugs often affect PC audio too!).
IMHO, the biggest pitfall of using a PC system and a DAC is the buggy SOFTWARE problems. This is one of the reasons why I still use software to control hardware to read redbook CD's rather than stream stuff from a hard drive using software. I simply don't trust the poor quality of engineering of software engineers (besides most programmers aren't even real engineers)
So iTunes 6 may work fine until you get the latest "upgrade" and then unwittingly you are suddenly listening to inferior reproduction due to a bug. (so even Steve Jobs can't get it right and you, as a poor user, don;t even know that something has gone wrong until you A/B something very carefully and your ears tell you something is badly wrong)
See also this