Under these conditions this is the expected behavior.
Normally when a a file is uploaded you don't loose connection like seen in your status log, due to this loss of connection FlashFXP doesn't get the transfer complete status message. Without it there is no way to know 100% for sure if the transfer was actually complete. Just because all of the data was sent doesn't mean that the ftp server received it. That being said, on reconnect it attempts to finish the file.
What you could do is configure FlashFXP (Options / File Exist Rules) to skip files of equal size.
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Hybrid Mode
