On the Avid side of things:
Avid brings in files either 'solid/fullscreen' as a video clip or it brings in a Real time Matte which contains objects (static or animated) that are meant to be put on top of (keyed over) existing video. For example:
If a lower third super was created correctly in a third party app outside of Avid, then it would have an alpha to make it keyable over your video inside of Avid. You would import (usually inverting the alpha) into Avid as a Real Time Matte. This clip would be put on a video track above your existing video and would be "keyed" on top. If you imported this same file by ignoring the alpha, then when this clip is put on top of your existing video it would not key. Instead the lower third super would have black or white as the background and be a "solid" piece of video.
If this clip you are wanting to import from Motion is not meant to be keyed but is meant to be used as a video clip, fullscreen, then you could ignore the alpha on import probably be fine if all areas of the screen look as it was designed. If you have black or white areas in your fullscreen video where you did not expect then you would need to go back to Motion and fill those areas with something, creating a 'solid, fullscreen' clip and when exporting you would not include any alpha channels.
It sounds like you rendered an alpha-channel file out of Motion. containing an audio file. In Avid, you have to make a choice: you can either import the video & audio (no alpha) OR you can import the alpha-channeled video (no audio). You can't import an alpha-channeled video with the audio.
The Fix -- don't render the audio in Motion with the video. Do it separately.
Why does Avid think like this? Who knows? I just deal with it.
KGAN (CBS) & KFXA (Fox) Cedar Rapids, IA