What causes the vacuum in my bento box?

The sealing effect is caused by pressure differences.

Once you put the lid back on, the warm air in the box cools, reducing the gas pressure inside the box below atmospheric pressure. So the atmospheric pressure outside the box tends to seal the box if there is contact all around the lid to prevent air moving between inside and outside. Water vapour condensing inside the box adds to the effect.

The same sort of thing can happen when you close the door of a refrigerator and the air inside cools, again leading to a partial seal.

Firstly, we must understand how microwaves work. The microwaves that are used essentially jiggle water molecules. Since most foods have water content in them... then that's why it works.

So water molecules jiggle around and since they are next to other pieces of food, they move too cause they keep bumping into each other. Thus, when all these things move, your food is "hot".

So have you noticed that right after you microwave food, its steaming? That's because the water has gained so much energy that it becomes a gas. Since your lid was not in the microwave and on the counter top presumably, its colder than your food and will thus condense the water vapor because it absorbs the energy from the water. This quick condensing is what I think causes the suction affect to happen.

If you microwave with the lid on, you'll see that your container might explode. Try microwaving food with the lid on and then put it in the freezer right away and see what happens. You'll probably get the suction affect very strongly.