If data is lost when closing flashfxp, the problem is most likely that flashfxp does not have permission to actually modify the files in the data folder location (because of UAC). The solution is to change the permissions of the current data folder location so that flashfxp can modify the files properly, or change the data folder location to somewhere that flashfxp does have permission to alter.
The suggested data folder location under Vista is C:\ProgramData\FlashFXP\ i believe.
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