When I set composite-items: true in config.yml, then restart the server, it sets the value back to false. Is there another setting that I am missing?

[20:20:32 INFO]: This server is running CraftBukkit version git-Bukkit-1.7.2-R0.
3-66-g43d8943-b3078jnks (MC: 1.7.9) (Implementing API version 1.7.9-R0.1-SNAPSHO
T)

[20:20:34 INFO]: [HyperConomy] Enabling HyperConomy v0.974.54
[20:20:34 INFO]: [HyperConomy]Using external economy plugin (iConomy ) via Vault
.
Running mySQL 55

You must disable HyperConomy before making changes to the config.yml
/hc disable
then make changes and re-enable:
/hc enable

Or make changes while the server is off, then start server.

Any changes made while the server/HyperConomy is on will be overwritten on server restart.