If BD-Rebuilder is not selecting the correct version, and you cannot deselect the stream with the director's commentary by previewing the movie in BD-Rebuilder (right click on the video once imported to BD-Rebuilder), then you can try running the movie through ClownBD to get the correct version. http://www.videohelp.com/tools/Clown_BD
Make sure to export as Blu ray in ClownBD. It won't take very long to do this process...nowhere near as long as compressing with BD Rebuilder. Test the output by playing the main m2ts file in Media Player Classic HomeCinema or VLC. Then compress it with BD-Rebuilder.