It seems more specific. The inconsistently is in the mid range of the greyscale and the lighter colors. That's also where the errors are.Is the inconsistency across the entire grayscale and colors, or more specific?
In my experience with the Manual Calibration workflow in HDR, CalMAN silently enables Full Screen Pattern Insertion behind your back when you get to the Meter Positioning page. If you've been working with it enabled, you might try disabling it to see if it makes any difference.