it's sick. that's what it is....the intonation 'at the bridge' will not correct all the issues. i have seen (and can't right now find) a neck with staggered frets (yeah, no lie. $500...but it claims to correct the neck issues, and one of the mags loved it).
this guy has the same issues i have. i can't come even close to his excellent explanation, because i don't have his technical background, but i hear this S$%t!!! AND IT DRIVES ME BONKERS!!!! years ago, before i had ruined my hearing with motorcycles, airplaines, complaining women, loud equipment and firearms, people who did not know me in our 100 yard by 50 yard 'office space' (old warehouse) would speak in normal tones, and i would later recount their conversation to someone or even them for some reason. they would say 'how did you hear me say that? you sob! did you have a bug in so and so's office?'. no, i hear things i don't want to hear....
when the guy in the article says his 'ears get tired', i have the same phenomenon. after an hour at a workable volume, i may start to hear things...usually, my mind focuses on some harmonic, or a string that has slipped. if B slips, i have to retune everything to 'compatibility', and to match with whatever cd or even my own looper tuning.
after readin ghis article, i now know why my korg tuner will sometimes go intermittent...i'll have to open it up, i suppose, and get the soldering iron.

i bookmarked this, so, when i get whackadoo, i can read it again and remember 'life is not perfect. tuning is not perfect. find a compromise, and live with it'.
what i am finding is 'removing the variables' (the tube amp harmonics, pedals, loose tuners, poor string anchoring, you name it) will allow me to have a session i enjoy. perfectionist...that is the same as 'ocd' or 'addict'. i am aware of this character flaw..i have more than i like to think about in common with Dr. Sheldon Cooper, sadly.
the 44magnum has saved my sanity, at least temporarily. i am finding that it plays nice with the looper. i'm enjoying my strat again...some of what this guy says is why i don't have the trem arm on the strat....another 'short putt to nutland' is what strat trem arms are for me.
http://www.endino.com/archive/tuningnightmares.htmli will tell you guys another thing...sincei have restricted myself to the 44, i am finding even more tones in the hagstrom than i did before.
MLJ, i have a little old vox digital amp...a da10, i think. it's a recording whiz....when i had everythig set up to go direct to computer, it's direct out was wonderful. the 'dubstep' that i put on soundclick was recorded using the vox. people just don't realize how useful some apparently small 'and not tube' amps really are.