When transferring lots of small files the "crash recovery" feature will reduce the speed at which the files are transferred.
From the FlashFXP menu, Queue > Restore Queue
Then from the Restore Queue dialog check the "Disable Crash Recovery" option.
With this feature disabled should FlashFXP or Windows crash your queue file will not be saved unless you manually save it.
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Also turn off disk based logging, This option reduces performance and should be used sparingly.
Options > Preferences > General Tab
Uncheck "Enable disk based logging"
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