There does seem to be an issue with demuxing here - clownBD/eac3to chokes (it appears to be caused by stream 6 / audio track 5), and tsMuxeR gives up halfway through.
Just to be clear, I'm not trying to make an MKV, just remuxing it to a BD folder format; the problem is with the initial demux.
It's just a bit frustrating since, as others have said, the previous DEs behaved just fine...