This is an issue that has occurred on multiple servers over multiple versions of the ATM9 Modpack, (though I have not played the mod in a single-player world so I can not confirm if this is a multiplayer-only issue or not).

It seems that after every time a multiplayer server reboots. the Functional Storage Drawer Controller has an issue where it unlinks a certain number of its drawers causing items going into the controller to fill other spots, instead of properly sorting into their own inventories.

This is what the correct sorting looks like while the server is running.

This is what happens whenever the server reboots.