You have to cover the top and bottom of the sphere in your panorama.
With this specific panorama, you can't do anything about the black voids, because you started with a 2.5:1 360 cylindrical panorama. So you're missing the top and bottom of the sphere, which it's filling in with black.
To make an equirectangular (and cube faces/QTVR Cubic) you need to cover the zenith (straight up) and nadir (straight down) views when you shoot and include those images in the pano stitch.
This is why panorama heads rotate both in yaw (around) and pitch (up-and-down).
An equirectangular is not just a 2:1 rectangle, it's depicting an entire sphere. The equirectangular projection represents a sphere by turning the longitude/latitude coordinates into Cartesian x/y coordinates. Cylindrical panos, by their very nature, never cover the zenith/nadir views.
See also: How are virtual tour photos taken?