On a whim this morning I thought I'd try resetting everything on the camera to factory defaults and see what happens. I only had about 10 minutes to experiment, but it seems the camera is now correctly recalling previously used lenses in the AFMA menu, regardless of the lens used, if the camera is power-cycled, or upon waking from sleep. Resetting the camera settings actually did not clear out the adjustment values I entered, but I did have to change the AFMA setting back to adjust by lens. Other than this change, I did not change any settings on the camera.
Looks like this is why Canon was unable to replicate our problem. I'm guessing their 1D X's are largely still on factory settings. Apparently some change that several of us made in the settings causes this problem. Looks like it is just a firmware bug that's even more subtle that I thought.
Everyone who has this problem, try resetting your camera to factory defaults, change AFMA to adjust by lens, and see what it does.