thank you for your responses, however, neither were the answers I was looking for. I also believe that you missed my point of using BPFTPD. Here's the case as it stands now (using full file download as examples, not resume) both going into the same folder.
NeoXed ... I have done what you have suggested and here are the results:
Site 1 to ioFTPD: ioZS -> file check = BAD flashSFV -> file check = BAD
Site 1 to BPFTPD: no sfv checker flashSFV -> file check = GOOD on 'site rescan' using ioFTPD ioZS -> file check = GOOD
Here is the information from Beyond Compare2:
Comparing files mo-amsw2.r05 and MO-AMSW2.R05.BAD
00DA8EF7: 86 C0
00DA8EF8: 16 A8
00DA8EF9: 54 00
00DA8EFA: 7D 64
what the implications of this are, I am not too sure. Basically, I would like to know the reason as to why when Site 1 fxp's to ioFTPD, the file turns out bad. But when Site 1 fxp's to BPFTPD then is RESCANNED by ioFTPD, the file turns out good.