Glenys Harris, of the Otago Potters group, asks :-
Why does food heated in a microwave oven cool quicker than that heated in a pot on the stove, even though both appear to be boiling?
John Campbell, a physicist at the University of Canterbury, responded.
I can think of two main ways which would explain this observation, but first the key differences between the two cooking methods.
When using a pot on top of the stove, the heat energy that cooks the food has to first heat the pot. Hence the pot or dish must be of a material that doesn't melt at the red hot temperature of the range element or gas cooker. Metals, being better thermal conductors, are the preferred choice for pots. When some of the water in contact with the bottom of the pot turns to steam, the steam helps cook the food. So the food and pot all heat to about 100C, the temperature at which water turns to gas. (If the water runs out, the food can be charred and raised to ignition temperature, a significant cause of house fires.)
In a microwave oven the electric field from the valve oscillates at about 2,500, 000,000 times per second. Water molecules oscillating at these speeds transfer the heat directly into the food. So the first rule of microwave ovens is that there must be water (or other electric dipoles) in the food. These oscillating electric fields have wavelengths of about 10cm so penetrate into the food by this sort of distance and can cook things up to a few tens of centimetre thickness. Good electrical conductors, such as metals, will absorb the electric waves at its surface hence containers used for microwave cooking must be non-electrical conductors, such as plastic, glass, porcelain, or dry pottery, which are also poor conductors of heat. The container only heats up by slow thermal conduction from its inner surface.
When removed from the microwave oven the container continues to heat, taking energy from the food which cools, until the food and container come to thermal equilibrium.
A second difference is that often we don't stir food in a microwave oven, except by rotating the food. To contain the microwaves to the oven, so we don't cook our eyeballs, the oven is a metal box with a window of small holes much smaller than the microwave wavelength. This means that electric waves are reflected off the walls and there are positions where the two waves cancel. I show these positions to classes by taking out the turntable and placing a slice of toast and grated cheese against one wall. There is no electric field (i.e. no heating) against the wall and also a quarter of a wavelength away so there are rows of unmelted cheese across the cheese on toast. (The evidence can then be eaten, especially at 8am classes.) Even with rotation, at any one time the food is being heated unevenly. When left to stand, the hotter parts cool down more quickly by transferring some of their heat to the cooler parts of the food and also to the container.
A careful scientist would test these theories using covered and uncovered pots but I am sure they are the nub of your observation.