How do I remove a roof? #Confused

So I've been expanding my base and have created a few 11x11 'rooms' and I've specified they not have a roof in Architect > Zone/Area > Clear build roof area - but when I click 'Toggle visibility of roofs' they still show as having a roof. The crops I planted are now dying, and the 'rooms' are still in shadow suggesting they are indoors.

I'm new at this game, so I'm probably missing something obvious. Can anyone enlighten me?