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Try unticking 'Use Passive Mode', 'Downloading' (NOT PASV) and Uploading (NOT PASV) under options in the Site Manager in FlashFXP.
I can't guarantee that this might solve your problem, as it's only a suggestion. However, i had problems backing up 'Buffy the Vampire Slayer', as about 3megs worth of files wouldn't copy over in the past when i attempted to back this game up But when i changed to the above settings everything was flawless.
Let us know if this fixes your problem.
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