Charles, you bring up some good points.. And I agree with George.. it's your system, your room, your ear, etc.. There are so many variables that it's tough to isolate why the change happens...
My philosophy has been that the room plays such a big role that when you insert various gear/cables/etc. to compare, you're really hearing how your room interacts with the subtle changes in frequency response.. or nodes or delays.. or changes in comb filtering.. all kinds of things that could make what you're hearing 'seem' like it was the component change but in reality was the way your room dealt with it.
To that end, I did my best to build a dedicated room to reduce the room's contribution. I also needed it to be comfortable and enjoyable, so it's not a lab... but it's as close I can come.
All that said, the room does still play a part in hearing differences. It's more apparent now than it was in any other room. Why there is a change is another story.. Is it because I'm hearing the true nature of Sylvania 12AU7's in my pre now? or.. the caps.. the interaction of the IC's.. etc. You can go on forever guessing because there's no way to truly isolate it. So, I do my best. The ONLY thing I changed is the PC so I know that changing that caused a certain effect, it is audible and repeatable. Does it apply to your system, I don't know.
One thing I noticed is that I can 'stack the deck' if I wanted to.. by tuning one component for another, I can trick myself (or others) into thinking that a sounds better than b. So, Kaplan's cables sound better if I use Mullard's in the pre... and Black Sand's sound better with RCA cleartops.. I know which cable will win when I do the swap. Also, the IC's make a difference as to which PC sounds best. So, I'm carefully aware of this and let people know what I've found before doing the swaps.
What happens is I decide x sounds best today but then I change something else, thinking 'well, a power cord shouldn't affect speaker cables..' But as things get changed, synergy-matching has started all over again.. and I've lost where it all went wrong... because the interaction within the system impacts all of it.. it is indeed a 'whole system'.
I'm trying to be very careful with the synergy thing. That's part of why I'm not touching the speaker cables. They're really good and I like what they do.. same with the amp, speakers, DAC.. etc. They're 'good enough' and I'd rather fine tune at this point.. which takes a lot of careful attention to what's really being compared... and how it impacts everything else.
-C