They may be placing brood in the center box simply "because" you gave them the three deeps... Don't know, but maybe if you scaled it back to only two, they'd start using the lower one like they're "supposed" to...
No matter really... as long as it's working the way you have it. ![Smile :) :)](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)