The datamap of a file is not be stored directly in the directory object anymore, but is stored as a name pointing to an immutable data in the network.
If what I computed in this post is true, creation or update of a small file (less than 3KB) costs 2 units from the put balance. For a medium file (between 3KB and 3MB) the cost is 5 units. This means we are very far from 1 unit = 1MB.
In the light of these figures you could compute the cost of your files. Maybe this could explain what you observe.