Scaler technically is not designed to do what you want in this scenario. Scaler is designed to recognize chords i.e. 2 or more overlapping notes. It will recognize single notes but it won’t keep them when you close Scaler and DAW. And Scaler is not designed to recognize timing information at all. The chords it detects are all timed with the beats you have set in preferences.
There is a related topic here - A Section with Single Notes Not Copied to Pattern?