This assumption must be wrong. Maybe not running it long enough. Otherwise you are suggesting the water pump control is failing except when you are manually setting it. Sometimes one wrong assumption or test result keeps us from even looking at the problem area again. Have you captured a graph of water pump speed vs temperature? Perhaps with radiator fan operation.
I got it figured out I do believe Driving the fans operate normally as should but the rpm moniter for the water pump will jump from 0 to 920 then in a few seconds back to zero with no heat in the car and temps reaching well above the normal 205⁰ If I go to active test and turn the water pump on it will run 3000k rpms and the heat magically starts working temps will drop and stay in the 190s While sitting idle you can hear the pump humming using a stethoscope but it has no flow. If I turn it on manually it will start to actually pump and circulate the water. My ten cents says that water pump is a dud Posted via the PriusChat mobile app.
Bingo........... Faulty new water pump straight from the stealership was the issue Picked another up yesterday and now we're perfect Posted via the PriusChat mobile app.