If I understand correctly, the water that is boiling after microwave heating
is above 100 C. The energy supplied by a microwave (klystron) tube is
funneled into a rather narrow surface layer. That layer can become
superheated since the the power input exceeds the power output from the
layer into the remaining mass of water. The fact that water has a rather
high specific heat exacerbates the situation. Thus when the surface layers
are superheated, the thermometric measurement probably weighs the surface
more than the bulk. Was the thermometer plunged into the middle of the
water or barely immersed?
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