Originally Posted by thegeneral

This is caused by pressure. The pressurization of the cabin is less than the pressurization as you descend. This is why when you drink part of a bottle of water at 36k feet, the bottle contracts as you near the ground. The pressure inside is less than the pressure around it.

The same thing basically happens to your sinuses as you descend. Some people are more prone to this than others. If you have this issue when you're healthy, I HIGHLY suggest that you don't fly with a head cold.