When you shoot in a common room, the floor and the ceiling are at approximately the same distance, and the scene is “vertically balanced”. However, in most scenes, the floor is much nearer than the ceiling (or, directly, the sky).
With such an “vertically unbalanced scene”, most, if not all, calibration methods (APG, PTGui, cameras built-in auto-calibration, Mistika's “Improve” functions) will try to converge cameras both at ceiling and floor at the same time. To achieve this, the calibration will result in all cameras pointing at the horizon with a slight pitch downwards, with the horizon resulting 1 or 2 degrees up from where it should be, (depending on the image content).
You can compensate this typical calibration imprecision by using the “Options->Vertical Offset” parameter, to place the horizon where it should be, at the center grid line of the 360x180 degrees LatLong stitched result.