You can only use KM to crop images that are in either the system clipboard or a KM named clipboard, so you need to make sure that the images in the folder you specify are read to a clipboard first. If you're working with multiple images, you should also make sure you don't write the same image name every time, or older images will keep getting overwritten by new ones:
Actually I spoke too soon. It’s putting the pages in the wrong order. It put page 2 at location 12, page 3 at location 23, page 5 at location 25 and page 6 at location 26.
How are the files ordered in the slash3 folder? If alphabetical order isn't getting the right pages, you could try other options like date created or date added.