i noticed this also in RC2. The transcoding with fuppes does not work. I edited the fuppes file to enable mkv transcoding support but no chance. When i access fuppes from my ps3 the service crashes with 'exited on signal 6 (core dumped)'. It crashes when a mkv file is in the folder/database without playing it (it doesn't matter if transcoding is enabled or not). When i remove the mkv file and disable transcoding the supported files by Ps3 playes well.
I would like to help to fix this. So i can test, provide logs, etc.