With the release of Studio One 5.0.1 on builds of MacOS 10.15, also known as Catalina, even with ATOM SQ set up correctly as a native device there are occurrences where the pad LEDs will not light up correctly.
This can possibly occur when loading in a virtual instrument, or when adjusting the range with the keyboard orientation, or switching through different scales. To remedy this, press the pad and it will most likely change the LED to the correct color. If not, try reloading the virtual instrument.
This is a known issue to PreSonus and is currently scheduled to be resolved.