The conical shape of the bottom of the boiler and the sizeable conical heating element provide more significant heat transfer and distribution to the wort during the boil.
As a result, when hot wort is drawn over the element as it goes to the pump, it retains heat and boils in the tube leading to the pump. This can cause an air cavity in the pump, resulting in the pump not starting.
However, this only occurs while the wort is boiling and the heating element is on. Turning off the element and restarting the pump will get the pump going again.
For the above reason, when sanitising the counterflow wort chiller, we recommend you do so at the end of the boil without active heat from the boiler.
Temperatures above 85°C (185°F) are considered to sanitise surfaces. Therefore, running the pump for a minute or two, post-boil will achieve the same result as during the boil.