I confirm that MakeMKV changes the chapter points. I'm not sure it puts them on I-frames, but indeed, most of the times, they are on a scene change. So, I don't worry about that, and anyway I can't restore the original timings.
Here is probably the last beta, unless someone finds a bug or makes an interesting suggestion.
Nothing really important has changed. Only some minor cosmetic changes, and the possibility to use the JPEG included in the MKV (if the original BD has an image in its metadata folder and if you have selected it in the MakeMKV GUI). If the Jpeg is present in the MKV, you can simply click the "From MKV" button in tab 4, and it will be displayed and loaded automatically. The "From MKV" buttons are disabled if there is no portrait or landscape image available.
Download:
BD3D2MK3D_v0.87b6.7z