Hi Rebecca,
Interesting results, "scanning under free scan mode for a single scan" ... does this mean you used the turntable mode or moved the scanner? It suggests you moved the scanner.
It might be interesting if you auto meshed the flat plate and see what deviation would you get then? Just curious.
I can see this in the CAD software, because if I scan a cylindrical object, I can draw a solid and superimpose it over the meshed image, and see the texture variations on screen.
What 3rd party software did you use?

Mike