Profile analysis graph not matching up with individual point deviations

[Ruda66]

The profile is out of tolerance on this cutout. Measuring from the top or the bottom says the individual points are too low. The datum is the bottom surface.

I usually don't use the graphical analysis but I pulled it up and it looks like I should've said the points are too high.

When I pull up this graph though it looks like the points are too high. What am I doing wrong? PCDMIS Profile Graph.PNG

[sealevel]

Do you have CAD for the part? Your profile looks like several manual hits. (not a uniform distance from each, vectors look funky) Is the surface a casting?

Measuring from the top or the bottom says the individual points are too low.

Do you mean you tried the profile reported first from the Datum and then from the top surface? (am confused)
Would help to see the code. Also, it's good idea to include the Min/Max when reporting the profile.