• I'm using 1.2.1. 
• If I craft a level 1 workbench, the usen /upgradewb to upgrade it to the highest level (not sure the level matters) moving a distance away while still within cupboard range, I can't craft a Miner's Hat. 
• If I spawn a level 3 workbench and repeat the same task, at the same distance, I can craft the Miner's hat. 
• Distance from cupboard is 5 foundations.
• I was able to duplicate this two times.

I assume something in the way the bench is upgraded using your Upgrade Workbenches plugin is breaking it.

What plugin has the command /upgradewb?

NVM found it. Give me a minute to look through it's code.

Looks like that plugin needs to be updated as it's not correctly attaching the workbench back to the building like it should be. You can replace lines 106 - 107 with the following and it will work.

workbench.OwnerID = originalWorkbench.OwnerID;
workbench.Spawn();
workbench.AttachToBuilding(originalWorkbench.buildingID);​

Thanks for the fast response! I'll give the plugin update a try.