Make sure you're tilting in pitch around the NPP point as well as rotating in yaw around it. You may have one arm calibrated correctly, but not the other on your panohead.
Having a separate piece of software, like Pano2VR, that can map your equirectangular to cube faces, so that you can then patch a specific face can also be helpful, if the head was over a featureless area--simple cloning/patching can erase the tripod.
If there are distinct features in the nadir, then you need to have additional nadir coverage aside from the shots on the tripod. Some people recommend moving the tripod, and then rotating the vertical arm of the head, so the camera is facing down for the nadir shot over the edge of the panohead (rather than the center of the tripod), but a handheld nadir shot (as long as the shutter speed is good) can work, too.
Don't include this "loose" nadir in the initial stitching in PTGui, but add it after the main alignment/optimization work has been done, and then use the viewpoint correction feature in PTGui to "patch" it into place. John Houghton has a good detailed tutorial on this methodJohn Houghton has a good detailed tutorial on this method.