We modified the inelastic bouncing ball model (IBBM) to account for the role of collision time ({tau }_{c}) in defining the dynamics of vertically vibrated confined granular systems. Although ({tau }_{c}) was surmised to be consequential for dissipative systems, previous studies on the accuracy of IBBM did not formally incorporate ({tau }_{c}) as a dynamical variable of the model, focusing instead on other factors during flight, such as air friction. We utilized the discrete element method (DEM) to study the role of ({tau }_{c}) in the granular dynamics, and to cross-validate the efficacy of our reformulation of IBBM to account for the effect of collisions. When the ({tau }_{c}) value is greater than that of ({t}_{0}), which is the first instance that the container acceleration exceeds the gravitational acceleration (g), the time-of-flight decreases, and the location of the bifurcation point shifts in the bifurcation diagram (time-of-flight versus dimensionless acceleration). We model ({tau }_{c}) as representing the range of uncertainty in the occurrence of ({t}_{0}). Assuming a separation of timescale between the dynamics of the collision between the center-of-mass (CM) of the granular system and the container, and the time-of-flight of the CM itself, we propose a supporting but separate model for the dependence of ({tau }_{c}) on Γ. The time-of-flight duration is determined when ({tau }_{c}) is known in the modified IBBM that now produces bifurcation diagrams which are in closer agreement with the DEM simulation results.