Oddly enough, I had the same problem with a USP 9c series pistol and found a unique pattern to it.
When I fired the 9c using commercial 115gr FMJ bullet from Wally World, the shots were about 2" low at 15 yards. However, firing 115 +P, 124gr NATO, or 147 grain ammo put the bullets right on target.
The way I figure it is that since recoil impulse acts on the gun during bullet travel, the heavier and/or faster bullets put the sights more on target than the lower recoil impulse of the light 115 grain standard pressure loads. Since the USP was designed as a combat pistol, it seemed logical to me that it would perform optimally with a stout full-power load.