Have you used another utility to compute the SHA-256 or MD5 digests of the binary files on both ends of the file transfer? It's not clear to me yet if your problem is that the files are not the same, and so something's wrong with the file transfer, or that the files are the same, and so something's wrong with your digest computation. Unequivocally prove the difference or sameness of the files first, then you'll know with certainty which of two different problems you must solve.
(I like md5deep for Microsoft Windows.)
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