Just discovered a similar problem myself but I don’t have FCP3 installed on my system (nor did I ever), except for Soundtrack Pro 3. I’m on a brand new 15″ MBP running the latest versions of Motion and FCPX.
My problem is that not all my audio layers are exporting; they just cut out and then audio picks up later. I have quite a few layers of short pieces of narration with separate audio clips interspersed, as well as video clips with their own audio tracks. Everything plays fine in Motion but when I export there are huge gaps. And if I export audio only the same gaps are there.
I actually prefer to do my audio editing in FCPX, completely replacing the Motion audio, but I use the Motion audio to sync the replacement clips. This is a major pain in the A!