It sounds to me as if you aren't updating the style associated with the scene. I imagine you have disabled the warning of style changes when creating or updating scenes.
First, select the scene you want the sections displayed, turn on the section cut and go to Styles to update the style by clicking on the large thumbnail in the upper left corner of the Styles window. This should help you get things straightened out in your LO file.
Next, go to Preferneces>General and make sure the box for Warn of Style Changes is ticked. In the future, when you create or update a scene after modifying the style, choose either to update the style or create a new style as appropriate. If you choose to do nothing, the style won't be updated and you'll create problems such as you report here.