Need som help with copying DVDs

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Here are the problems I am haveing, the movies tend to have what I call hesitations (where the video for less than a second) and sometimes part way through the movie the directors commentary kicks in, even though I have only selected the main part of the movie. Currently I use AnyDVD and CloneDVD2 to rip the movie and Nero 7 Ultra to burn it. When I play it on my computer there are not any hesitations but sometimes still the direstors commentary. My computer is about 6 years old with a 1600 AMD Athlon processor and 512MB DDR RAM with a brand new Sony DVD burner. I think it may the speed of the processor that is causing the heistations. You suggestions and ideas are greatly appreciated.