I have " stop motion keyframes" checked in Preferences and every time I set a keyframe it sets it as a motion keyframe. I’m using Harmony Premium 16, Mac osMojave. Not sure why this is happening. I have to constantly click on the keyframe and select " stop motion keyframe ".
Maybe something got corrupted in your user preferences.
To test this try renaming the user’s preferences folder for
the software while the software is closed (otherwise it will
just duplicate what is already there):