The export should match the contents of the timeline.
Try deleting render files and exporting again.
If the problem persists, delete the application preferences: To delete preferences, hold down command and option while starting FCP X and click Delete Preferences. The application will start in a default state, and open an "Untitled" library.
Reopen the library you were working on, set the preferences the way you like them, and try again.
If the problem persists yet, Please run Etrecheck and post its full report here.
Use the "additional text" button and paste the report into the text box.