I experience the phenomenon often. I think Macdadtexas (and the poster to whom he referred) has the best single answer in terms of gear. Not only are there different power draws throughout the grid at different times of day, but there is a different level of electronic interference in the air (including household) and in the grid. If I had to pick times when my gear (generally) sounded the best, it would be early in the day--say 7:30-8:00 a.m., and a couple of hours after dark. So, even though I don't have one, a power conditioner seems like the one thing that could level off SOME of the inconsistencies. I've been eyeing the newest Shunyata conditioners (especially the Triton).
The other thing to blame is simply our moods. Plenty of people have alluded to that. Kind of like a biorhythm thing. In my scenario both of the timeframes I mention are either before the tension of the day is built up (a.m.) or when I have escaped it at night. Sometimes my system sounds the worst when I am trying to use music to get away from the BS/stress. Of course, nothing has changed about the gear--it's all in my head (stress, etc). There are times I just cannot get real joy out of my gear and some of those times I even blame the gear! It's idiotic, of course. I'm sure that even after I manage to assemble some sort of undefined "ultimate system" (for my means, anyway)I'll still have plenty of moments where the music is still not totally in synch with my head. It's those moments when it IS that I treasure.