An engine system includes a first module that determines a cylinder of an engine to be in one of M prediction types and generates a distance from intake signal indicating a number of prediction steps the cylinder is away from an intake stroke. M is an integer greater than or equal to 3. A second module determines a cycle type of the cylinder. The cycle type indicates a number of combustion cycles the cylinder has experienced from a last restart of the engine. A cylinder air charge module estimates an air mass within the cylinder based on the distance from intake signal and the cycle type.