This is my observation
One factor involves distance. The thought is that if you select a chest to be moved from one location to another then a unique link is created between that object and the ghost object created at the new location. However all the Hearthling seems to knows is that a chest needs to be place at that location and a box is box and will select the closest one. The further away an item is the less priority it seems to receive. Hearthling seem to select task that are closer to them, so the far away crates are less appealing than restocking an item on the ground at their feet. They will eventually go get the far away crates as soon as nothing else is grabbing their attention but they are not above taking shortcuts. Another factor that seems to be involved is the number of items in the world. Small population with few items seem to work as intended, but once you get over 2-3 thousand items is when I notice this behavior.