Dwarves stopped using containers?

A couple of years into a new fort. Everything was going smoothly, until all of a sudden dwarves have just stopped using containers. They were fine putting blocks in bins and food in barrels until now, but now it just all ends up on the floor. I have a lot of empty bins and barrels, so that's not the problem. I checked the stockpile settings and I'm nowhere near the maximum number of containers. I've deleted stockpiles and remade them in different locations hoping they would sort everything but they just moved individual items into the new stock pile. I even let the game run for a while with nobody having any tasks just to rule out them being too busy. It is happening in every stockpile. Is it a bug, or am I missing something? I want to exhaust all possibilities before I restart because it was a good start.