Phase separation kinetics of a binary (A,B) mixture contained in a thin film of thickness D induced by a quench from the one-phase region into the miscibility gap is studied by simulations using a Cahn-Hilliard-Cook model. The initial randomly mixed state (50% A, 50% B) contains a concentration gradient perpendicular to the film, while the surfaces of the film are "neutral" (no preference for either A or B). In thermal equilibrium, a pattern of large A-rich and B-rich domains must result, separated by domain walls oriented perpendicularly to the external surfaces of the thin film. However, it is shown that for many choices of D and the strength of the initial gradient Ψ(g), instead a very long-lived metastable layered structure forms, with two domains separated by a single interface parallel to the external walls. The transient time evolution that leads to this structure is interpreted in terms of a competition between domain growth in the bulk and surface-directed spinodal decomposition caused by the gradient during the initial stages. A surprising and potentially useful finding is that a moderate concentration gradient perpendicular to the film does not favor the layered structure but facilitates the approach toward the true equilibrium with just two domain walls perpendicular to the film. This mechanism may have useful applications in producing layered materials.