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The click you are hearing is a thermal fuse that is designed to protect the magnetron. It opens when it gets too hot and closes when it cools. If the fan is running, there should be no reason why it is getting hot enough to open. So, either the fan's air path is obstructed and it cannot cool the magnetron or the magnetron is failing. The fan is shown in the picture at the link below. There are actually two sides to it. One side cools the magnetron and the other provides the ventilation for the cooktop. Are you able top remove the unit from the wall and take the outer cabinet off to inspect the smaller blower for any issues?