I've never seen or heard of such an issue. Considering all the info you provided regarding the stability of the tuning and the brand new state of the guitar, I can only think that maybe you're holding the guitar too tight, applying too much pressure to the neck while you fret, so you even get a stiffer feel to it. How tight are the neck screws? Is there a gap in the neck pocket? Check those things and try to play as smoothly as you can for a whole session, and see if it still happens. I know it's a shabby advice, but believe me: depending on how tense I am due to whatever factors, my playing and the way I feel the guitar changes RADICALLY in a gig or even a rehearsal.