This is my second fortress, so it's possible that the mistake is on my side, but my problem matches the problem discussed here:
http://www.bay12games.com/dwarves/mantisbt/view.php?id=8293

Bins exist and are sitting in furniture stockpiles. Finished Goods Stockpiles are using NO bins, despite being set to use various numbers of bins. Multiple stockpiles were created as I tried to understand what might be going wrong, and all of them consist of individually stored items.

This game was launched with with the DF Starter Pack, with DFHack enabled and using the Spacefox tileset.