TripleHBK said:
From the beginning this looked like a problem with the torrent creation itself.
It's more likely that the problem was caused by corruption of the data as it was being uploaded to the seedbox.
SFTP should always be used to upload/download data instead of regular FTP.
FTP transfers cause data corruption, but if you upload/download with Filezilla in SFTP mode instead of FTP mode, the .md5 files should match up after the data is transferred.