Bob, you should be able to turn off the Auto Rotation feature in the camera settings menu. Then, it is simple to select and rotate all the images at once into the preferred orientation in Bridge. Otherwise, you can individually check the values of the orientation tag of nadir and zenith images and rotate to portrait (-90?). You may need to edit the Bridge metadata preferences to enable the display of the orientation tag.
Another option is to avoid shooting with the camera pointing directly up or down. Tilt the camera away from the vertical a bit so that the gravity sensor delivers reliable up/down data and the zenith/nadir hole is still adequately covered.
John