Well, it is well known that Full-SBS causes many aspect ratio problems, as there is no standard to follow, and each player reacts differently. It's why there is an option to change it : Settings -> Full SBS/T&B Aspect Ratio. But for Half-SBS, things are normally much easier. BD3D2MK3D follows the well established standard for Half-SBS and Half-TAB, and it's the first time a problem is reported. So, undoubtedly, your equipment is the culprit.
That being said, it is possible to modify the aspect ratio stored in the files used to do the conversion. (You can't use the Settings menu, as it is taken into account only for Full-SBS.) The aspect ratio is present at two places. The SAR (Sample Aspect Ratio) is stored in the video stream (and therefore it cannot easily be changed after having computed the 3D video stream). You can edit the --sar 1:1 argument in the __ENCODE_3D.cmd file. I suppose that for Half-SBS, you should try --sar 2:1, but I'm not sure. You may also try to simply remove that argument completely, and let the projector decide.
The second aspect ratio is stored in the header of the video stream in the MKV container. It can easily be changed even after having computed the video stream. It is in the __MUX_3D_OPTIONS.json, in the section about the video stream. You will see this:
Code:
"--aspect-ratio",
"0:16/9",
It is easy to understand that it should be sufficient to modify the 16/9 string in the second line. Again, I don't know what value you need to use. Try 16/18 or 32/9 and try also to remove completely the two lines.
To mux the final movie without having to recompute the 3D video stream, just launch the __MUX_3D.cmd file. It will recreate the same MKV but with the new aspect ratio. But remember that this will not change the SAR in the video stream.
I suggest to do your tests with a short clip. You can also change the number of frames to compute (the --frames argument) in the file __ENCODE_3D.cmd to compute only the beginning of a long movie, and test it rapidly.
Please let me know the values you have to use to obtain the correct result. If it's not too difficult, I will perhaps add an option to change that values from the GUI. Thanks in advance.
Good luck !