this has nothing to do with the flasher, with md5sum i'm trying to help you verify that your downloaded image file is not corrupted.

you put md5sum.exe and the eMMC .bin in the same folder, open a command prompt, "cd" into that folder, and run
the output you should be getting is a certain value which has to be the same as in the MD5SUM file from the download page (this is not the .exe you downloaded, but a file at the same location where you downloaded the image files and the flasher).
if the output is any different than what is contained in the MD5SUM file, then your downloaded image file is corrupt and you should download this file again.