DVD shrink is no longer updated so it can't handle the copy protection on some of the new movie releases you maybe trying to backup, so use DVDFab decrypter first instead.
Use DVDFab to rip the files to your HDD, it will create a VIDEO_TS folder and put all the video files in it. DVDFab is a whole movie ripper only, so you're getting everything on the disk ripped to you're HDD, once DVDFab is done, run DVD shrink. Use DVD shrink to open the files created by DVDFab (use the open files tab and browse to the VIDEO_TS folder created by DVDFab and choose it), at this point shrink will import the files, use shrink as you normally would to create your backup.