If I do a ...
components = MorphologicalComponents[img, 0.3, Method->"BoundingBox"];
followed by a ...
binCounts = BinCounts[Flatten[components]];
I find that there is a prime number binCounts. Regardless of padding and other edge effects, shouldn't each entry in binCounts be the product of two integers; viz. the height and width of a (non-overlapping) bounding box? Perhaps the sides of the bounding box aren't parallel to the axes? If so, can one ask MorphologicalComponents for bounding boxes that are?