What is the movie?
By default CloneDVD always selects the longest title.
I always preserve the menu's and on a few rare occasions, CloneDVD has selected the wrong one (longer) and the menu did not work. I went back in and selected the shorter one (by about 1 min) and it worked fine.
This is using the movie only mode, and checking the preserve menu's.
If you say you only loose a few percent by selecting both, then take that safe route.
If you have a DVD R\W disk you can experiment and try doing one at a time with preserve menu's and see if they both work. If the longer title fails, the shorter one was the right choice for that particular movie.
After each test, erase the DVD, it will cost you nothing but your time.