The prj file alone does not help here. We would need the pcb_new file.
A remark on zones: They only fill if something is connected to them. So make sure you have either a via or a pad that connects to the net within the zone. (on the correct layer of course.)
Also look at the clearance and minimum width settings. Maybe these prevent the zone to connect to the pads you expect it to connect to. (Zones have their own settings in their properties dialog.)