I know you have tried really hard to describe the problem, but from anothers view it is not well understood.
Perhaps try breaking down the project and start with fewer tracks from FCP first and see what the result is. No one is doubting their might be a "bug" but generally the bug is the user of the applicaton, not the code.
Since Soundtrack is not intended to be a MultiTrack Editor, there might be some incompatibilities in your thinking and the actual capacity of the application?