I was backing up a double disc of some TV episodes when I noticed that although there are four eps on each disc, there seem to be two copies of each episode appearing in the CDVD2 menu - each exactly the same length.
Okay, I thought, I'll try dropping off the second copy of each, mounting the ISO on a virtual drive and then seeing how it plays . . .
Well, seems to play okay, but the thing is dropping off the second copy doesn't appear to have much impact on the final quality percentage - although there is a slight difference depending on which ones you select?
Can anyone explain my little mystery?

Sure. There might be multiple titles on one DVD, which share the same video material. In theory you can put the same movie on one DVD many times, but change only small parts (ending, beginning, title sequence in different language, ....)

CloneDVD2 Quality bar is clever enough to detect "shared material".

In the example above, deselecting one movie will only change the quality bar a little, because only a small part (e.g., the alternate ending) was left out from the shared video material.