To compare two bitmaps, you must designate one bitmap in the comparison as the baseline and the second bitmap as the result. While you may have many bitmap files open in the Bitmap Tool, at any one time only one bitmap can be set as the baseline and one as the result. If you want to set new baseline and result bitmaps, you must first un-set the current assignments.
These designations are temporary and at any time you can set and reset a bitmap as a baseline, result, or neither.