Good question. Honestly, I don't encode in T&B mode, and I have not used the old conversion method (w/o 3D-planes) since a while. I do not support or develop it any more, and I should have removed it already. (If I have kept it, it's only because it offers the possibility to convert several subtitle streams in one shot.)
Anyway, I did only the GUI and I am not the author of the exe that is used by the old method (suppe3d.exe), and if it doesn't work as expected, I can't fix it because I don't have the sources, and the author is not active any more. So, if it appears that it doesn't work correctly, I will almost certainly remove it.
Can you confirm that your movie is correctly encoded in real 16:9 half-T&B (1920x1080)? If the black borders of a Cinemascope movie have been cropped, it is normal that the vertical position of the subtitles is wrong. Same thing if the movie is encoded in Full-T&B.
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