During installation you need to select "Custom data folder" and leave the path so it's identical to your FlashFXP installation folder.
If you changed the folder path FlashFXP will set a registry entry that is shared by both installations.
Based on my understanding of your intended configuration you should not have any of the following registry keys.
HKEY_CURRENT_USER\Software\FlashFXP\3\DataFolder
HKEY_CURRENT_USER\Software\FlashFXP\3\AppData
HKEY_LOCAL_MACHINE\SOFTWARE\FlashFXP\3\DataFolder
HKEY_LOCAL_MACHINE\SOFTWARE\FlashFXP\3\AppData
At your own risk you can try deleting these registry keys.
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