It seems like the problem is that if you use the snipping tool to save to a file that already exists it only modifies as much of the file as is required so that the new image you saved is visible - the rest of the file's data is preserved. The problem is saving to a file with more information than the cropped information requires - the original images information "overflow" isn't removed. So if you're saving to a new file it's fine, there's no extra information.