When you installed FlashFXP you selected to user Per-User Settings. In this configuration you'll need to create a new windows user for each different configuration.
In order to undo this you need to open regedit
Browse to HKEY_LOCAL_MACHINE\SOFTWARE\FlashFXP\
Delete the key "APPDATA"
Copy the files from "C:\Documents and Settings\user\Dati applicazioni\FlashFXP" into your FlashFXP folder.
Before continuing make sure FlashFXP is correctly loading the right settings.
Now create a new folder for your second set of settings and copy the FlashFXP.ini into the folder.
Then you need to create a windows shortcut to FlashFXP.exe and make the startup path point to your new settings folder.
If you did everything correctly it should work..
This should be in the help file and explained more clearly, Linkster?
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