I did the same thing. I think perhaps the tutorial is wrong, that you're supposed to unpak everything to a different folder? The guy who made the tool says later in the thread: "Don't unpack the .pak files to the game Data folder, as it can have interesting side effects and overrides changes that the official patches do. I suppose I should add a warning about that ..."
Wups.
Yup. Basically if you exctract the paks in the data folder,the game will load each resource twice.
It'll work in the majority of the cases, as most resource types were designed to be overrideable, however it may not work properly for some files (eg. stuff in the Public\Content\ folder), that's why you are seeing duplicate items in the resource browser.