sometimes wheels take a while to settle in.
back when Cupertino Bike Shop was importin Cinelli's and other nice frames, they would build the wheels and let them sit for 6 months til the frame came in.
this acted as kind of a 'burn in' period for the rims, so that after a final touchup after 6 months, they would stay pretty straight.
i bought a bike online a while back , as usual, the rear wheel came in out of whack. torqueing the spokes helped, but the wheel was still a little out. what happened was the rim was physically bent, so that in order to get it back, the spokes had to be tightened, then ride for a few months, the re-true, ride for a few months, gradually the wheel worked itself back to being straight. then the axle broke so i bought a cassette type wheel and have finally joined the 20th century.