I use a Nikon D50 and found that this image rotation stuff confusing at first. In the menu of the camera you can turn on or off image rotation. With image rotation on - some programs will see the pictures rotated, but if you look at them with other programs they will not be rotated. Really, the image is not rotated, but appears to be. For the sake of my sanity, I turned off the image rotation in the cameras menu. I just use my favorite program to rotate it for real (Photo Mechanics - Tools - apply rotation to jpegs).
Hope this helps.
Bill