There is no errors in the console.

When I spawn an item with world.spawnItemNaturally(location, itemstack), sometimes the items can not be picked up. It sometimes happens, sometimes it doesn't. It also won't call PlayerPickupItemEvent and the items will not merge with other items.

Typically this happens several hours after server restart.

Utilising https://gist.github.com/aadnk/5563794#file-cancellationdetector-java I am able to determine that no plugin is cancelling PlayerPickupItemEvent and the event is not being called at all on these specific, random items.

Players have suggested that it happens when a chunk is unloaded and reloaded, but I have unloaded chunks and reloaded them and the item will still work sometimes.

My exact plugin code hasn't changed in months and was working prior to updating to the latest Spigot. Previously my old build was at least a month old, and was on a Spigot 1.8 build. Unfortunately I do not have the build version.