I had exactly the same problem, and I managed to make it work by running QuickBMS after dumping the entire contents of the Xenoblade .iso into its own folder. Apparently, you can't just extract a solitary .pkb file and run QuickBMS on it; the .pkb file needs to be located in the correct directory within the contents of the .iso.

You can also try running "quickbms_4gb_files.exe," which comes with QuickBMS. That's the one I was running when it finally worked.

What are you planning to do with the models anyway? If you figure out how to vertex edit them, please let me know.