Just like the previous Transformer movies before it, Transformers 3 Dark of the Moon has the 99 track protection as well.

For more information on this particular protection system, you can visit the following link: http://www.tools4movies.com/2010/11/dvd-catalyst-4-non-standard-dvd-protection-popup/

After scanning, DVD Catalyst will display the track selection dialog for this movie:

It will likely have the wrong track selected, so leave this open, and start Windows Media Player or VLC, and get it to actually start playing the movie.

If you use Windows Media Player, it will display the tracknumber at the top left of the video panel. If you use VLC, go to “Playback” in the top-menu, select “Title” and you will see the correct track highlighted:

Close VLC/Media Player, and in the track selection of DVD Catalyst, enable the track number you found and click OK.

Then change profiles and or settings to your liking, and start a conversion:

and thats it.