sounds like they burned through their stores because of the rain. We just discussed this at my club meeting last night. They eat it and the queen immediately fills it with eggs. Maybe rotate the bottom box to the top and under the box of foundation. The bees like to work up.
Bees will consume stores during inclimate weather both to survive and to rear more brood, when the honey and pollen is gone they will cannablize the brood, eggs, larva, and any pupa still in the white. A hive can starve to death in less than a weak if the weather remains bad and the hive continues to rear brood.
Happens a lot in the spring. Most spring hive losses are due to starvation due to rapid brood buildup and bad weather.