The LEDs on the boost v3.1 operate the same as the remote's LEDs.
Meaning one is for the positive voltage of a waveform, and the other for any negative voltage. They are not indications of voltage for Out 1 and Out 2, and will reflect the overall voltage swing of both outputs when combined.
So if you have a waveform with a built in positive offset like above, you will only get the positive LED lit.
As another example, if you use two waveforms from each output that cancel out, neither LED will be lit.
For more details, please check the link: