Do you have Clipboard Auto Transfer enabled? This option is intended to start transferring the queue after connect if a ftp url to a file was passed.
I think what's happening is that FlashFXP thinks you're passing a ftp url to a file and attempts to start the queue after connect. Make sure your ftp url ends with a / or \
Or if you are indeed passing a ftp url to a file this is the intended behavior.
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