I recently attempted to rip a couple of new 3D titles into my library using the latest version of MakeMKV (1.15.2) and ran into a problem.
The discs rip without error. The client plays the result without error, identifying the file as a 3D disc. The projector properly goes into 3D mode and activates the glasses but the image on the screen is not 3D. It is as if the images being played for the left and right eyes are identical rather than one of them being an offset image. This is a new issue as I have successfully ripped many 3D titles before. As a test, I redid one of my previous titles and the result displayed the same problem. I then tried going back to previous versions of MakeMKV to see when the problem manifested itself. I did not still have a copy of 1.15.1 but I did still have 1.15.0. Ripping the discs with 1.15.0 resulted in files that played correctly.
So, it appears that in either 1.15.1 or 1.15.2 something broke in the handling of 3D discs.
If it helps any in pinpointing the problem, I will point out that making a backup copy of the disc using MakeMKV, then using tsMuxeR to create a .m2ts file from the appropriate playlist also results in a file that plays correctly.
My rips are done on a Mac. 3D files are played back using Plex for Kodi on a Raspberry PI running LibreELEC.