This paper provides comparisons between experimental data and numerical results for impulsively started flows in a three-dimensional rectangular lid-driven cavity of aspect ratio 1:1:2 at Reynolds number 1000. The initial evolution of this flow is studied up to the dimensionless time t = 12 and is found both experimentally and numerically to exhibit high sensitivity to geometrical perturbations. Three different flow developments generated by very small changes in the boundary geometry are found in the experiments and are reproduced by the numerics. This indicates that even at moderate Reynolds numbers the predictability of three-dimensional incompressible viscous flows in bounded regions requires controlling the shape of the boundary and the values of the boundary conditions more carefully than needed in two dimensions.