I never did get the ftp session log to better understand this problem. Until I do there really isn't much that can be done.
However:
For clairification though the "Transfer is complete. Closing data connection." message is a ftp server reply. Since the file is an upload the ftp server doesn't really know how big the file is, it just assumes it's complete.
The "Transfer failed" message comes from FlashFXP and it is the accurate status of the transfer.
One thing you can do is configure your file exist rules to skip files of equal size, that way if the file is in fact complete it wont be overwrote.
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