I've been noticing recode grouping titles, too, on quite a few disks recently; I don't know if it is a change in the way Nero works or if I just haven't encountered disks like this before. I notice this in "recode entire disk" and "recode main movie". In my cases I'm pretty sure it has to do with branching or multi-angle presentations - such as on Alien 2003 Director's cut (like Abyss or T2, it has two versions of the film) or as on Bridge on the River Kwai and In the Bedroom (which have titles and credits in a couple different languages).
It seems to sometimes treat both threads as different sets of data even when most data is shared; the original title file sizes reported often add up to more than a dvd can fit. Yet I can usually make sense of it all by using the "remake a dvd" mode which splits the titles up so I can see what they are, and so far I've made the right guesses in choosing a recode method to get the results I hoped for.
Again, I never noticed this before (the last NVE release) so I don't know if something changed or it's just my luck of the draw.
Hope that ramble helps.