It's because, in generation 1, it was a normal type move, so it was physical. Then, when the dark type was introduced, it became a dark type move. All dark type moves were special at the time, so the damage category changed to special. In gen 4, the physical/special split happened, where the damage category was done for individual moves instead of by type, so it once again became a physical move.
Also, why does Bite change it's damage category?