CAM Compare reports a whole small board as being different rather than isolating the specific points that are different.
CAM Compare combines adjacent differences to minimize the number of issues that the user must examine when inspecting the report. For a board that is small relative to the default box size, all differences on the whole board might be grouped.
Change the configuration parameter ia_box_size to 100 (mil) for small boards, so that the individual differences are reported. On large board this setting would cause CAM Compare to report many more individual differences - many of them from the same source.