Happy you found a solution, since eac3to isn't available for Linux and Mac I won't integrate it into Hybrid.
That said, ffmpeg might be capable to extract those subtitles,... properly. (No Hybrid doesn't support using ffmpeg to extract subtitles from transportstreams&co.)
For me, it is not a problem, because it is (according to my so far experince) a very very rare situation to have such "tricky" streams.
I have found the following very rare problems with Hybrid as well:
- sometimes Hybrid keep the dts-hd stream even if I check automatic dts-hd to dts downmix (very rarely!);
- sometimes Hybrid remux an other audio stream into the mkv container (e.g. I select hungarian, then remux czech - very rarely!);
that's all. Negotiating these above very small problems Hybrid is my number 1 program for conversion my BD-s.
Within a month I will complete my complete 2D and DVD collection and hoping you can help converting my 3D collection as well.