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"Manuevering rocket malfunction?
Software "glitch"/Hacking?
Pilot error? (Was re-entry automtated?)
What other causes might there be?"

Main causes I can see are: 1) loss of integrity of heat-shielding. An amazing amount of air rubs over the shuttle each second during re-entry, under high pressures. When pressure increases, so does temperature...even before the molecules start rubbing against the surface of the shuttle. If a large enough area becomes open to the heat, it can melt the shuttle hull, or even incandesce objects on the other side of the hull.

Communications is lost for a portion of re-entry, because the friction is so great that the atmosphere, and portions of the shuttle skin are ionized (i.e. electrons gain enough energy that they leave orbit around the nucleus).

2) Loss of structural integrity. The shuttle is under a great deal of stress. If significant components shift they can cause instability, or if they come off, they alter the aerodynamics of the craft as well as stripping the craft of some of its heat shielding.

3) The shuttle became unstable. The shuttle must come in in a very specific configuration, otherwise it can begin to wobble, or spin, or slow down too fast. If the shuttle wobbles out of parameters, it can place immense stresses on the craft in ways that it was not, and could not be, designed for. If the shuttle slows down too fast, it heats up too fast.

While there is some fuel in the shuttle during re-entry, it is a rather small quantity, the re-entry being non-powered. The shuttle is designed to slow down by a series of banking maneuvers gradually increasing the drag and extending the flight distance while within the atmosphere.

There may be other things, but those are what first come to mind. Obviously, all three happened, the question is which caused the others to happen.