the problem is tapas also has a file size limit, and allowing the full dimensions of 940x4000px of a PNG can sometimes cause the image to go over the 2mb size limit. So croppy tends to chop the comic slightly shorter to help guarantee you won't run into the file size limit- I don't remember what the max length is, I can ask my husband.
If you're getting more than 40 images than you're file is either too long to begin with, or you're feeding it too many small files that are just long enough to require croppy but are short enough that croppy is making some of the slices small.
For example if you feed it a 940x4500 picture, and say croppy cuts pictures to a height of 3000 for tapas(Again I don't know how high it actually is I'm just using this as an example) then you'd get an image that is 940x3000, and another image that is 940x1500. Which is fine for one image, but if you upload 21 of these suddenly you get 42 pieces and it's not going to fit the 40 image limit. However if you had combined all these images into one long strip croppy would have cut it to to 32 pieces which would have been fine.