I had to return my .40 compact for the same thing. They said the wrong sights were installed, and shipped it back. Seems to have taken care of the problem for the most part, but my 9mm fullsize is now doing the same thing.
If you examine the barrel to slide fit, you'll probably find that the barrel tilts slightly downward, and that the greater the distance from target, the lower the gun seems to shoot. I think it's an aspect of the design, but to find out for sure I did a set of shots on a single target with the same point of aim from different distances, starting at about 2 yards and backing up a few yards per shot until I reached 25 yards. There was a steady decline in the point of impact with each shot at the same point of aim, so clearly the barrel was in fact tilted downward. Still is, in fact, but the sight change corrected for it to a large extent.