Hi Jamie,
I am getting the exact same behavior on two different FCP/Motion systems.
If you export to Motion from the FCP TL and you have audio that is linked to video, then the audio will go out to Motion and then back in to FCP. If you add additional audio while in Motion, that new audio will not come back into FCP.
If you add linked audio and video in a new Motion project and then bring that project into FCP the audio will not come across.
This does work properly when you bring a Motion project into DVD SP from Motion, even if you add unlinked audio in Motion, it too will come across to SP.
--ken