iOS.xml profile for Plex Media Sever. Copying this to iOS.xml and iOS-iPhone5,1.xml in Profiles allowed AC3 audio from iOS device to AppleTV 3 device. If you are running Plex on a Drobo5N then the location of these files are located in /mnt/DroboFS/Shares/DroboApps/plex/Application/Resources/Profiles

iOS.xml

<?xml version="1.0" encoding="utf-8"?>
<Client name="iOS">
  <TranscodeTargets>
    <VideoProfile container="mp4" codec="h264" audioCodec="ac3,aac" context="all">
      <!-- Inspired by Handbrake's profiles -->
      <Setting name="VideoEncodeFlags" value="-x264opts bframes=3:cabac=1" />
    </VideoProfile>
    <VideoProfile protocol="hls" container="mpegts" codec="h264" audioCodec="ac3,aac,mp3" context="streaming">
      <Setting name="VideoEncodeFlags" value="-x264opts bframes=3:cabac=1" />
    </VideoProfile>
    <MusicProfile container="mp3" codec="mp3" />
    <PhotoProfile container="jpeg" />
  </TranscodeTargets>
  <DirectPlayProfiles>
    <VideoProfile container="mp4" codec="h264" audioCodec="ac3,aac" subtitleFormat="ttxt" />
    <MusicProfile container="mp3" codec="mp3" />
    <PhotoProfile container="jpeg" />
  </DirectPlayProfiles>
  <CodecProfiles>
    <VideoCodec name="h264">
      <Limitations>
        <UpperBound name="video.width" value="1920" />
        <UpperBound name="video.height" value="1080" />
        <UpperBound name="video.bitDepth" value="8" isRequired="false" />
      </Limitations>
    </VideoCodec>
    <VideoAudioCodec name="ac3">
      <Limitations>
        <UpperBound name="audio.channels" value="6" isRequired="false" />
        <UpperBound name="audio.bitrate" value="640" isRequired="false" />
      </Limitations>
    </VideoAudioCodec>
    <VideoAudioCodec name="aac">
      <Limitations>
        <UpperBound name="audio.channels" value="2" />
      </Limitations>
    </VideoAudioCodec>
    <VideoAudioCodec name="mp3">
      <Limitations>
        <LowerBound name="audio.samplingRate" value="32000" />
        <UpperBound name="audio.samplingRate" value="48000" />
        <Match name="audio.samplingRate" regex="32000|44100|48000" />
      </Limitations>
    </VideoAudioCodec>
  </CodecProfiles>
</Client>