Since I updated to 2.009, Plex will transcode every file, even the most basic ones (720p, mp3 stereo, no subtitles). Before the update, these files would have been direct played. As soon as I go to the settings, and change any setting (no matter what), I get the correct behavior (transcoding only if necessary). I have to do this each time I use the app, i.e., I start the app, and have to go to the settings, otherwise it would always transcode.
I have to mention though that I'm using a very old version of PMS, because my old Mac Mini cannot run newer versions.
Plex app: 2.009
PS: Thanks for the great app! :)