The problem is MakeMKV selecting the wrong playlists (1,2 and 3) with too many chapters (the correct playlists with the right number of chapters are indeed 850, 851 and 852 as cyborg mentioned!), there really should be a way to manually select the correct playlists in MakeMKV, like you can in DVDFab!
Unfortunately, I can confirm this is still present in 1.12.2. The work-around I used was to simply backup the disc, open the files within MakeMKV and start removing the errant .mpls from the "PLAYLIST" folder, ensuring that MakeMKV only "saw" the ones I was interested in.
It's been a while since anyone has posted to this thread but I found a way to convert the Avatar Extended Collector's Edition to mkv using makemkv, although it's a bit of work.
Open the disc in makemkv and find the mpls files used define the Titles that have too many chapters (mine were 00001, 00002, 00003)
Look at the detailed output where mpls files are skipped because they are identical to those you found in the titles. It will look like: "Title 00802.mpls is equal to title 00001.mpls and was skipped". Mine were 00802, 00850, 00851 for theatrical, re-release, and extended
At this point, restart makemkv and don't open the disc. Instead, perform a Backup of the disc to your hard drive
After the backup is complete, go into the Backup to /BDMV/Playlist and replace the mpls files you found in the Titles with those that were skipped. I replaced 00001 with a copy of 00802 that I'd renamed to 00001 and so on.
Finally, in makemkv, open the file /BDMV/index.bdmv from the Backup on the hard drive
You'll find the chapters are correct and the mkv can be created properly
I know this is an ancient thread, but I *just* ran into this issue and couldn't find an answer anywhere online. Most posts I could find concluded that this was some kind of DRM and either recommended using DVDFab or simply ended without any kind of answer, so I created an account just to help anyone who stumbles across this in the future. I ripped the Theatrical version from both my regular Avatar Bluray (35 chapters) and my Extended Collector's Edition Bluray (57 chapters), synced both streams in two VLC windows side-by-side and let them run. They stayed in sync through the whole movie.
So the answer is yes, the same version (i.e. Theatrical) has a different number of chapters depending on the source. I can only assume the additional chapter markers on the Extended Collector's Edition Bluray are there so it can seamlessly add the extended content while using the same scenes in all 3 versions of the movie.
