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** Fixed at ArcGIS 8.2 **
After clicking 'Fit to display' on the Georeferencing toolbar, and adding some control points, clicking 'New Map File' does not clear the transformation from the Georeferencing session. When the raster is re-added to ArcMap, the transformation is still applied.
This is a known limitation in ArcGIS 8.1.
Click 'Reset Transformation' on the Georeferencing toolbar before clicking 'New Map File.'
Alternatively, exit and restart ArcMap to clear the transformation.