Don't worry. I appreciate your help, and I ask you explicitly to continue to notify me of the discrepancies or bugs you find. Especially with the problems related to the subtitles, that I can't check easily due to my lack of appropriate hardware. Each time I want to check the accuracy of the 3D subtitles generated by BD3D2MK3D, I have to hardcode them on a video, and of course, that means that I have to recompute the whole movie with x264. It's a long operation, and therefore I can't do many tests. For that reason, I need the help of everyone.
Anyway, I should have examined the Depth values in the temp 2D XML files with more attention. The fact that there are some warnings about undefined depths when converting subtitles coming from the original BD is an evidence that something goes wrong. I have just finished to encode Avatar during the night, but this time I've used a frame rate of 24fps instead of 23.976 to translate the timecodes of the subtitle stream to frame numbers. In other words, I have assumed that the subtitle streams (at least the XML streams converted from the original SUP file by BDSup2Sub) use drop frame timecodes. If that assumption is correct, the result should be slightly better than my previous encodings, and the obviously wrong depth of a couple of subtitles (that I have previously attributed to slight authoring errors) should be correct now. I still have to watch the movie, but if it's the case, the fix is probably easy. It is sufficient to modify the frame rate in my code. But I must be sure that the fix works for every movie, and in other words that there is no "hidden" drop frame flag in the header of the 3D planes. As you can see
here, Bigotti5 helped me much to decipher the content of that header, but there are still unknown bits in the header. It is possible that we don't have yet the information necessary to correctly compute the frame numbers if the frame rate to use depends of the BD.
Anyway, first things first. I will watch my last encode of Avatar and if it is convincing, I will release a new beta soon. Then, you will have to test if the 3D subtitles are correct.
BTW, you can already do some tests at 24fps if you wish. Use 3DBD2MK3D to generate the project, but re-generate the 3D subtitle stream(s) with the Convert subtitles to 3D (with 3D-planes) tool. In the tool's dialog, simply change the frame rate from 24/1.001 to 24, and overwrite the original 3D subtitle stream. You can then encode normally (or, if you have already encoded the h264 stream and you don't need to hardcode the subtitles, just launch the _MUX_3D.cmd batch to generate the final MKV). And enjoy the movie, hopefully with good 3D subtitles. :-)