I received a 5.1 ac3 file from the projects sound guy for burning to DVD. The issue is that when imported into Adobe Encore the DVD Transcode is set to "automatic". This is usually something that happens when the file is non-compliant with DVD standards. In this case though I can burn a Blu-ray disc with the same 5.1 audio on the settings, "Don't transcode" and it works fine.
From what I have read of Adobe Encore Transcoding it appears that it could have something to do with the bitrate of the audio, but, due to my inexperience at Authoring of DVD's I can't say for sure.