Well I ended up removing the old roost and installing a new bigger roost (about 3.5x1.5 inch) with rounded corners, and moving it to the other, higher side of the coop and taking out the poo box.
It worked! Usually when I shut the coop up at night there is at least 4-5 chooks on the roost. The youngest chook tends to like the nest boxes still, but once I kick her out and block it off she flies up to the roost. I think over time and as they get bigger and stronger at flying they will all use the roost every night. Here's a new photo: