Ive been using FileZilla portable for a while and i have noticed one thing. When you connect to a shell (via ssh2) you have to accept the key (you can choose to allways accept it which i did). When i use filezilla on another computer you have to accept it again. So i think this "setting" is stored in the registry. A reason for that is maybe that filezilla uses FzSFtp.exe to connect to shells and that this file havent been included in the nsis script.