The section around the stem is usually the most stubborn and deceiving. I always give the tube stem a push up into the tire to verify it isn't caught on the rim. It should push in easily before fully inflated. If not, something is pinched.

I also inflate to 40 psi, pinch the tire saidewalls together with my index finger and thumb around the circumference of the wheel to verify the tube is seated properly in the tire. If I can't clearly see the rimstrip, something's wrong.