When you open a Final Cut Pro-created movie in Soundtrack Pro, you may come across a situation where your score makers don't appear in Soundtrack Pro. This can happen if you open a Final Cut-exported movie with score markers in Soundtrack Pro, delete the file, go back to the original movie project in Final Cut Pro, edit or add score markers, re-export the movie with the same name, and then open the file in Soundtrack Pro again. Soundtrack Pro will not show any changes or additions you made to the markers.
To avoid this issue, change the name of the movie when you re-export it from Final Cut Pro. Then open the renamed movie in Soundtrack Pro.