I have seen many audio exporting issues of the years with Motion. This I think will only get worse as it gets more embedded into FCPX. The solution really is to not do any audio editing in motion at all. Either export the pictures into fcpx or some editing app, and recombine with audio there. Or create a finshed audio bed and import into motion ( thats what I do)
I only use audio in Motion for timing. Then I export video only, and match it back to the video in QT 7 Pro or FCP X.