I have most certainly experienced this, and there are two factors I take into consideration.
First of all, perception. Some days our moods our just better, which can lead to more confidence in our playing. Conversely, if we are feeling down, we are more apt to be down on ourselves, and our playing.
I've done litmus tests in which I film myself improvising, and then don't watch the clips for several months or even a year. I make a note to say at the end of the clip whether I felt good or bad about the playing.
There have been numerous instances where in hindsight I thought I was playing well, but at the time thought the opposite (and vice versa).
I try to keep this in mind as last night I laid down an acoustic guitar track for a new song I am recording. I didn't have that euphoric feeling after that I sometimes do. But I'm inclined to believe that's mostly perception. Not that what I recorded was great, but if I 'try' again tonight, would the results be noticeably different? I don't think so.
We've probably all had a time or two when we caught lightning in a bottle when the red light was on, but for me at least, those times, are rare.
So for me, I do feel my good days vs. bad days is often a case of perception.
The other thing I am very careful of is my hearing. I live a very clean lifestyle. I joke that I have to keep my hair at least somewhat long, or I would be the world's biggest geek! But - my one vice, used to be (and still occasionally is) cranking up the headphones.
The tones we are able to achieve with our guitars, as well as drum software, loops, etc. are unprecedented. I have been guilty of cranking up my tracks to concert levels and just basking in the quality of sound we can now achieve at home (which we couldn't do with our 4 tracks).
I have tinnitus but it's not nearly as bad as friends of mine. So I just try to be very careful about volume (though sometimes I just can't help it!).
Last week a friend was in town from Canada and we hit a karaoke bar. It was way too loud, and as much flak as I got for being a killjoy, I waited outside. It wasn't worth exposing my hearing to those levels.
You seem to have some scientific basis for your differences, singtall, in that you can see or hear frequency changes. All I can gather from that is, perhaps the acoustics of the room are affecting your tone?
I know when I mix, so many factors can change the balance - speakers, room, volume.