Since the scans are images (correct?) they should be transferred in binary mode, so the local size should be identical to the remote size, was the size different in the prompt?
When you setup a scheduled transfer task its 100% automated and not necessary to add FlashFXP to the windows startup. The task is run via Windows task scheduler.
In addition when run as a scheduled task FlashFXP runs minimized to the system tray.
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