With me, it took awhile, but it finally sunk in that no rewriting of CloneDVD code etc or any method of ripping of an ISO with another program and burning with Write Existing Data could EVER make CloneDVD preserve the original (discreet, intelligent) layer break because that one function is outside of the ability of ANY transcoding program. It is not the design or purpose of a transcoder to preserve the original layer break. It is the wrong software to use for what I have labeled a 1:1 mirror copy. It's design is to alter (not preserve) an original to our preferences.
There was a member (we all disliked him, I think he got banned) a while back who kept telling me that a transcoder can't do this or that but he was so socially inept and had such an irritating style of communication and bluntness that I just ignored anything that he posted to me. But he was correct. A transcoder like CloneDVD has the express purpose of changing the original for purposes of removing unwanted titles and tracks ... because of this ability, it can NEVER make a true 1:1 copy of an original simply because of it's inherant design. Notice that CloneCD has no ability to remove titles ... it is not a transcoder and thus can make a 1:1 mirror. And THAT is what I want for DL backups.
Tru doesn't like to suffer the extra stuff (warnings, previews etc) and would rather suffer and indiscreet, "automatic" placement for the layer transition. But AnyDVD removes the User Prohibited limitations of the original so on the backup, one can just remote-jump past the trash and get to the menu. This is most excellent! ... and a small price to pay for keeping the discreet original layer break. ... for me anyway.