First do a clean install of Fetish - make sure you're not copying into an existing folder or anything.
Next, if windows are still gone, and it occurs on all characters not just one, backup/rename your characters' uisettings.xml files (the full name format is Server_Character_eq2_uisettings.xml, with Server and Character being what they are for the character in question). If that solves the issue, then you probably had something messed up in your uisettings; just rearrange windows back to how you like them.
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