I have the exact same issue. It happens when i export and reimport AIFFs even without as much as touching it with Soundtrack. Problem lies in FCP, Quicktime or audio drivers IMO.
Try this:
1) export your timeline as AIFFs from FCP
2) re-import these AIFFs into FCP
3) place them accordingly into timeline
Is it out of sync? Mine is. Just a few frames, but unpredictable (i.e. moving those Aiffs in timeline for a fixed number of frames doesnt help)