CPD is very sensitive to the condition of the surface. The condition of the surface can change between the scans due to adsorbtion of gases or humidity changes.

Try to do your CPD measurements in controlled atmosphere. For example, you can enclose the instrument in a sealed box and flow nitrogen through the box.

If your system drifts off of the resonance of the cantilever, due to temperature changes, for example, you will measure slightly different CPD values. Check that you are still on resonance.

Also if you have tip changes from picking up atoms or molecules from the surface, this will also change the CPD. Use a reference sample and check the work function of the tip.