Problems recognizing midi

I’m trying to generate chords for a simple 16 bar 2 part quantized 4/4 midi file. Everything has been quantized to quarter notes with durations of multiples of a quarter note . The top part is a simple melody with one note at a time, the bottom part is a slower moving bass chord note, one note at a time. I’ve removed all non-note info (aftertouch) from the input midi file. It is a type 0 (one track) file.
I first tried dropping the midi file onto the detect screen. It generated something with recognizable notes but many were repeated and there was no rhythmic relationship to the input. Nor any recognizable chords added to the input.
I switched to putting the input midi and scaler on the same Reaper track. It generates a recognizable output in the same timing as the input file, but on playback, where there are held notes at the end of some measures in the input, only a quarter note is generated , so the resulting timing does not match the original. In addition, although the display shows a lot of complex chords (set to triads), none of these exist in the midi capture output.
Should the output of hitting play after record be the same as the midi input (minus the missing measures which were apparently deleted because of no chord change) or should I hear newly generated chords? Am I just supposed to write down the names of suggested chords and figure out a way to incorporate them with my melody? Should I only use a single note midi input ( I assumed if I added a one-note bass part it would provide more information for chord formation.)

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?

Thanks very much for your explanation.