What are the differences? What are the size before and after the process? Can you use HexEdit, GHex or other similar program to examine the content and tell us the differences between the file before and after process?
Also, try to send/receive file with smaller size, maybe text file with 20 characters. I ever had problem sending files over network, the results didn't match if the file size is over hundred KB, but ok for small files. After inspection, the problem was hardware issue - the network cable.