Many Vista users are encountering this problem. The settings should migrate automatically but Vista has some issues that can cause migration to not be able to see the original settings. The installer will not delete existing settings without copying them into a time stamped backup folder but the location to store these settings has been changed for better Vista compatibility.
Look under Help/About, Details tab to see where FlashFXP is looking for data files.
Then locate your old sites.dat and other FlashFXP data files, this is likely under "C:\program files\flashfxp in Vista". Copy the sites.dat and quick.dat files from this location to the FlashFXP data folder. Other files can be copied over as needed also.
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