Redo the test! Make sure that the shutter speed are right. My suspicion is that the camera when it controls the aperture it doesn't do it correctly. The level moved a bit more than it was supposed to. When in A and M mode the aperture is set via the aperture ring and the aperture stop down level in the camera would move all the way. The setting on the aperture ring limit the aperture to stop down to only the set aperture. In P and S mode the aperture ring is set to minimum aperture, the stop down level would move just enough to stop down to the aperture that the camera determines as correct. This level may have moved a bit further than is was supposed to.