Got it, what you should do is use the "Trim" feature in DVD Ripper to extract the scenes you want, one at a time, into individual MP4 files. This will go faster if you convert the entire movie to a VIDEO_TS folder on your HDD and run the conversions to MP4 from that.
To set all these up and run as a batch, set up the first scene using Edit->Trim, then click OK. Now use the Copy Source function (right click in the Title line) to re-load the full movie Source again and repeat the Edit->Trim steps for the second scene and so on until you have them all listed, then press Start. See the screen capture attached. To make them into a single MP4 at the same time, just click on the "Merge" button.
