are you sure the logos and things are within the menu? i’ve seen them where once you click “play” from the menu you’re launched into the logos and trailers since they are shoved at the beginning of the main movie titleset.
if the above is the case then it’s been discussed before about clonedvd2’s inability to cut by frame (as dvdshrink does) as oposed to by chapter (its current capability).
it had to do with the fact that clonedvd2 always offers you the option to retain menus whereas with shrink if you do any reauthoring the menus go bye-bye. clonedvd2 cannot offer the frame by frame cutting that would allow you to snip out logos and trailers that are embedded in titlesets while still maintaining the “preserve menu” option.
if the parts you’re talking about are indeed within the menu itself then I’m not sure what the explanation is.
Like Taylor30, I’ve seen it mentioned numerous times that Clonedvd2 is a “1-click” program in essence. it’s meant to be simple. hidden advanced options might be a decent idea though unless there’s some actual technical reason that what you’re asking can’t be attained (as I mentioned above)
I think if you’ll search you’ll find numerous “want lists” and “feature requests” for clonedvd2 and it seems like despite all of the wishlists that have been posted, the developers have a specific idea of what clonedvd2 is and what it isn’t.
I’m looing forward to hearing the “official” word on this though!