The structure of lamellar poly(styrene-block-methyl methacrylate), denoted as P(S-b-MMA), diblock copolymer films on neutral poly(styrene-random-methyl methacrylate), denoted as P(S-r-MMA), brush surfaces was examined as a function of annealing time and film thickness using neutron reflectivity and small-angle neutron scattering. Upon annealing, microphase separation occurs quickly with perpendicular and parallel lamellae emanating from the neutral and air surfaces, respectively. This initial growth is followed by a slow increase in the amount of parallel lamellae with a concurrent decrease in the amount of perpendicular lamellae as the samples are annealed further. After long annealing times, the amounts of perpendicular and parallel lamellae do not change significantly. The mixed lamellar structures show a strong commensurability trend with film thickness having a period equal to that of the natural lamellar period. This is explained through the preferential formation of s(1/2) disclinations having PS cores which dictate the observed commensurability trend. The preferential formation of these defects was observed by field emission scanning electron microscopy on films predominantly comprised of perpendicular lamellae.