David--
First thought, could this be the result of banding from a clogged nozzle? In the long dimension (direction of print head travel) you might be measuring in an area where the clogged nozzle doesn't cover, but where you're measuring in the short dimension (direction of paper feed), you might be measuring in an area where there is banding.
Second, wow wide is the border around the step tablet? The 361-T typically uses a 3mm measurement aperture, so you need an absolute minimum of 3mm (1/8") of area to measure, and ideally, 1.5x to 2x that to take into account positioning inaccuracy, flare, and light piping through the substrate. Is the rubber on the bottom of the measurement head (that makes contact with the OHP), in good condition, or is it hard or cracked?
Also, have you taken repeated readings from the exact same place? How much variation there? Is it possible you've got some electrical noise problem that's causing the light source to vary or the noise is coupling into the electronics?
Just some more things to look into...
Good luck.
--Greg