Sounds like you didn't update the style before updating the scenes. Section display is a style setting. If you change anything related to sections you must update the style or create a new one in order for the change to be remembered. If you've made a change to the style and haven't update it, the thumbnail for the style will show the curved arrows.

If you don't update the style before creating or updating a scene you should get this warning.

When you get it you need to make a decision. Either save as a new style or update the selected style. Don't just choose Create a new style every time you get it because you may wind up with a bunch of identical styles which makes file management harder. But if you choose to Update the selected style the change will be applied to all of the other scenes that use the style.
If you aren't seeing this warning then at some point you must have selected the Do nothing option and ticked the box to prevent this warning from showing up. You should re-enable the warning since it appears you aren't managing the style changes on your own.