I've had one gun that had legitimate accuracy issues out of the box.

It was a Ruger Single Seven in 327 Magnum. I was getting no discernible group(and even some off the paper) at 7 yards. There were also a lot of noticeable bumps and "catches" in the action. Several other people shot it, and no one was able to get the gun to group.

After 100 rounds, I looked the gun over, and there was a noticeable amount of wear in one side of the forcing cone. I called Ruger and sent it back(on their dime). As per the report, they replaced the pawl and recut the forcing cone. They also test fired it at 15 yards with the ammo I specified, and included the test target(about a 1.5" group with 6 of the 7 shots making a big hole). They also had it back to me in a week and a half(I wish S&W would take some lessons from them). Since then, I've been able to shoot it much better, and feel pretty confident that any issues are my fault.

I recently bought an S&W m52(c. 1978, but new in the box) that shot terribly on my first range trip. With that gun, I'm positive that the problem is related to the "nut behind the trigger" as the saying goes.