Hi Duncan, DVDAE cannot convert the full DTS MA to FLAC, only the core part. This explains why you have only 48kHz files.
Better option is to direct demux the files. This gives you the full DTS MA files. After that you can use Audiomuxer to convert to FLAC. Perhaps this solves the missing centre channel as well, assuming htere should be anything in the centre channel.
Or you can use Foobar2000 with its DTS Decoder plug-in to do the same (if you have or use Foobar already). Foobar is faster than AudioMuxer.