Hi @kkatzer it sounds like Scaler 3 is working as intended. Currently (as of Scaler 3.2) only the main track chords respond to MIDI trigger notes. However one of the recently revealed features in the upcoming Scaler 3.3 update is the ability to bind multiple tracks, which should allow you to accomplish what it sounds like you are trying to do, where while tracks (melody track etc.) accompany triggered main track chords.
Whilst this feature is currently in development, Davide posted a quick first look video recently on the forum. Scaler 3.3 First Look - Multi-Bind Performance (early preview)