Rat Brain registration:  resolved the quality problem by adding and additional (5th) landmark at the back of the brain in the Eyes Plain.  Apparently the 4 Landmark configuration was too close to a Coplanar that was causing the Affine registration to fail.

Additional BrainBack landmark

Affine registration result:  Transformed CT overlaid by the MR-template landmarks.

CT layer (Green) overlaid with transparency on top of the MR layer (Red)