I think that any rotations made in mc11 makes pics rotated the wrong way in mc12. All you have to do is clear any rotation values for yuor pics, in the rotation field in the tag window, and then they will be displayed corrrectly.
Also, (the way i understand it), any rotations you perform in mc (using the rotate tool) should physically rotate the image, so explorer etc. should see them the same way.
However, if you use a number in the "Rotation" field, rather than the rotation tool, explorer won't show them rotated, although photoshop etc would be able to display them correctly (because they judge the orientation based on the tag info).