the hardware is top notch, so i doubt the tuning peg is the issue here.
you're probably onto something regarding the nut though. it's indeed not sitting as good as it does with e.g. .49 strings in D standard.
it's like this: i can get it in tune and intonate right for doing chords on the 1st fret upwards, but then the open string will be sharp. conversely, if i tune it flat to compensate for the open string being sharp, powerchords on the 1st fret upwards sound out of tune.
i really really have to be careful with my picking strength to avoid this. which strikes me as odd, as i can beat the shit out of my higher tuned guitars. gotta tune the lowest string sliiiiightly flat of course (like, 5 cents down) but it works fine.
it's obviously a technique issue too....fretted notes require a different picking technique than open strings, and i'm well aware of that.