I think I'm there at last 
Basically tried installing a 2.9.1 version (on a clean alternate install) - just got original properties screen with no checkboxes
npm installed duff 2.9.3 - got checkbox properties with none pre-checked
npm installed 2.9.1 again - back to original screen
npm installed new 2.9.4 - got checkbox properties with all pre-checked
So hopefully that's a valid test sequence
New PR with 2.9.4 on its way - can you change to 2.9.5 when finally merged into master
Going for a lie down 