If you create a new layout from the bottom of the right panel in setup mode, and apply the same layout options for flow headings, does that layout do what you expect it to?
If so, the chances are that you’ve manually overwritten/adjusted the text in the text frames of your original layout. This results in page overrides, which mean that subsequent changes to layout options won’t affect those pages. There’s not a lot you can do about that in Elements, aside from not fiddling with the text in frames until you’ve got your Layout Options nailed down.