If you are displaying multiple header images in a slideshow, the system will automatically save the same crop across all images so that they align nicely within the header section.
For the best user experience, the aspect ratio for each image in the slideshow must be the same. The crop tool bases the aspect ratio on the first image that you upload to the slideshow.
Make sure that all of the images you upload to the header are approximately the same size (you can find a guide to resizing images at the link below) as this will make it easier to adjust the crop for all images to the correct size.
Follow this link for full instructions on How to Crop Your Website Header Image.