First, what are your Export settings in AE. For DVD (not BD), I strongly recommend elemental streams, i.e. a video-only DV-AVI Type II file, and an audio-only PCM/WAV 48KHz
16-bit file. Import the DV-AVI video-only file into En as a Timeline. Import the WAV audio-only file into En as an Asset. From En's Project Panel, drag the Audio file to the appropriate Timeline. This has always worked ...