"He who marches out of step hears another drum." ~ Ken Kesey
Did the new one come with the dark blue lens diffuser and is it still glued in position over the hole ? Also you can try adjusting the angle of the photocell, so it is not aiming directly at the lamp.
Is there a dark piece a glass on the inside of the hole that is shown on the bottom photo ?
Brett, I think your problem may be CELL SPEED. for each channel there should be a cell speed setting 1,2 or 3.. we use 2. that will significantly reduce the countdown speed when exposing.
another thought... is there a potentiometer on the keypad or board that you can adjust ?
Did you get the new parts from Nexmark by chance ?
This may be a kind'a crude suggestion, but assuming that you have to rethink your light units with this new set-up anyway, what about covering part of the sensor? Would that trick the integrator into thinking it needed to increase your times?