Switching on fancy leaves only makes outer leaves see-through, this is generally a great optimisation because it doesn't affect gameplay, however for the large oak trees, hidden, opaque leaves can completely conceal wood from all sides which is a very frustrating mechanic if you want to clear a forest. The player can appear to have removed all wood, but the floating leaves will remain. A couple of solutions to the problem could be to have 3 options for leaves, with an even higher option which disables this performance feature, remove the isolated logs from the generation of these specific trees, or you could prevent the leaves from being opaque within these specific trees if fancy graphics is enabled.