When converting the srt-subtitles using
3DSubtitler.exe, do you select Vobsub idx/sub as output?
If so: is VobSub support enabled in BS.Player?
(rightclick >) Options > Preferences > Subtitles > [VobSub]
Also: is "Allow intermediate filters" (and "Enable advanced graph building") selected under
(rightclick >) Options > Preferences > Filter management [General] ?