I'm afraid I have to report that moving from 1.03 to 1.04 has broken playback of OGG files for me. Did the audio folders ever show a ##--TRANSCODE--## folder, because that isn't showing up, but I can't remember right now if it ever did. Regardless, I tried with both Mencoder and FFmpeg as the transcoder. Previously, Mencoder worked perfectly. The files do show up as "PCM" in the XMB, but both transcoding engines result in "The data type is not supported".
Also, I too am still getting most of my sound out of the right channel only when transcoding from DTS to LPCM.
A couple notes: I fully uninstalled 1.03 prior to installing 1.04, and I don't use the media library.
The video side of things continues to work near flawlessly for me, though. Good work on that!