The Lyot Project near-infrared JHK coronagraph achieved first light on the Advanced Electro-Optical System (AEOS) in March 2004. Optical pupil plane imaging at video rates from this coronagraph provides data on atmospheric scintillation and quasi-static pupil intensity variations. We examine the effect of these variations on coronagraphic performance. Early simulations suggested Strehl ratio reductions of the order of 2–3% due to residual uncorrected phase aberrations in H-band. We find that static or quasi-static pupil illumination non-uniformity in I-band reduces Strehl by $\sim$2%. A lower bound on the effects of dynamic illumination variation over the pupil is also $\sim$2% in I-band. Some of the static intensity variations in the pupil are due to pinned deformable mirror (DM) actuators. We simulate the effects a pinned actuator has on the coronagraph. The resultant speckles in simulated coronagraphic images show similarities to some Lyot Project PSFs. This highlights the importance of knowledge of the pupil in next-generation extreme AO coronagraphs in order to realize the predicted photometric dynamic range of their images.