Those black areas mean your source panorama does not contain full spherical coverage. A 360° cylindrical panorama records the view all the way around horizontally, but not necessarily straight up (zenith) and straight down (nadir). When PTGui converts that into equirectangular or cubic output, the missing top and bottom of the sphere are filled with black.

So in this case PTGui is not creating an error—it’s showing missing image data. You generally can’t remove those voids from this panorama unless you manually retouch/fill them, because the scene was never captured there.

To make a true equirectangular panorama or complete cube faces without holes, you need to shoot and stitch images that cover the full sphere, including the zenith and nadir. That’s why panoramic shooting often uses a pano head that allows both horizontal rotation and upward/downward tilt.