A firewall/router will manage socket connections and close connections that have been idle for a long period. When the router closes the connection it doesn't inform the client or the server. When the transfer is completed FlashFXP tries to send a command and that's when it determines the connection has been lost.
There really isn't much you can do about it.
FlashFXP does contain an option to help eliminate this problem but reports have shown that in most cases it causes more problems. The options is located at Preferences > Proxy Tab > Send noops during transfer.
If you encounter any new problems you will need to uncheck this option. This option will cause different compatiblity problems depending on the ftp server software.
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