Are you sure that the dll file is in the working directory of the sqlite shell? Are you sure that there is an entrypoint with the name sqlite is using to initialize the extension? Are you sure you are running the same sqlite.dll in both cases? Or rather a custom sqlite.dll with "included" uuid.c in one case and whatever windows regards as sqlite.dll in the other? If you need to have a specially built sqlite library, you should statically link it to your application.