Your first back-up file set is seemingly 2X the size given the rounding error as you posted.? I haven't used the AVRDUDESS GUI.? Perhaps you did 2 back-ups to the same file and the dudess appended the files?? intel HEX as ascii, you should be able to look at the file(s) and see if it was appended.? See if there are 2 EOF records.
Rgds,
Gary