In Smartripper select ALL the vobs.If you try in movie mode you won't get everything.I saw the same problem 2 days ago at my friends house.In movie mode you get, say, title 1 then multiple chains, and you can only select 1 chain, which is quite small.In file mode select ALL the vobs you need. If need be put Power dvd in file mode and play them 1 by 1 after you've ripped them all, deleting any you don't need.Once you've done that then you can run the vobs thru dvd2avi, vfapi then cce. Load into Spruce create chapters at the start of each episode and make buttons from chapter points.
Hope this helps