Well I've found that one of those programs will do the job. If one can't completely do it then the other used after it will fill the gap. If you're not having success with the 2 progs, then try another such as suggested earlier in the thread or search here:
http://www.videohelp.com/ or here
http://www.videohelp.com/tools
As for dvd-r media, it depends upon your burner. Particular brands will tend to prefer particular brands. I use a Pioneer 109, & I use TDK & Verbatim. These are 2 of the 3 best tested with this brand of burner. As for other brands, you'd need to search for the results. There's a site that lists test results for particular brands tested v's media. Media availability is an issue b/c in different places different media is available.
BTW you can extract particular chapters also & later join them using dvd2oneX. But it's something I've never tried. Also, I find that it's generally the Xtras on a disk that seem to have the greatest problems for extracting for some reason. So if you can extract the main chapters then that's all you need.