OK, sounds a bit strange, as I have had no probs at all.
Have you checked that you have definitely ripped all the files ? i.e. have you compared the ripped folder to the Original disk, to make sure it's identical ?
Sorry to ask that, if you have, but often the simple stuff is under our noses sometimes.
Also, have you managed to successfully process any DVD in Full disk mode, i.e. could it just be something odd with these particular disks ? ..... are they Episode disks ?