A guess, that you have your audio and video on spearate timelines. An asset won't show up in the orphanage; for it to be there, it is a timeline.
When you bring the files into Encore, use "import as timeline," and, for each timeline, select both the m2v and wav that belong together.
To fix this In your current project, drag the wav asset to the timeline with its video. If you created a timeline for the audio only, delete the audio only timeline.