I was looking at and comparing the PS3.conf file to the file types currently supported by the PS3 and the files don't match up! Some of the mime types are incorrect and needed to be corrected, LPCM won't play at all when converted to so something needs to be fixed there, I've split apart the DTS and LPCM from WAV since they each have their own mime types (LPCM has 4), and the flv format works just fine so I could add an entry for it.
Really, it looks like the conf file hasn't been updated in quite a while.
If you're looking for backwards compatibility, perhaps there's a way to tell the PS3 firmware versions apart from one another to choose the best conf file for the job.
In any case, FLAC files aren't transcoding properly, so something's broke somewhere and I can't seem to find it.