The only thing i can think of is, did you define an ip in "bind sockets to this address" located in the Preferences / Proxy Tab?
If you bind this to an external ip you may encounter problems with local file transfers.
If you think it might of been an option you changed you can delete the flashfxp.ini in your FlashFXP folder or "\Documents and Settings\<USER>\Application Data\FlashFXP\" to reset FlashFXP to default.
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