all i can think of is the standard checks. make sure neck tension is set properly, make sure the neck isnt warped, make sure the frets are all the same height...etc...
if all other frets sound good and the rest checks out, either raise the nut by putting in some glue with bone shavings (or plastic) into the high E string rest slot, or file down the fret until it rings true.
again if all other notes on the other frets sound good on that string ...id file down the fret myself. sometimes they move and raise up and get loose. tap it down or file it id say.
edit: i have my first fret set to .01 clearance. i think the neck relief at the 12th fret isnt much more than that either. just a good check.