BO2s and BO3s (and most likely all other things that use LocalWorld.setBlock) don't recalculate skylight. At first I thought that I simply missed a change in Minecraft's obfuscation, but this doesn't seem to be the case (relighting is still done using world.A(x,y,z)). Vanilla trees, which don't use LocalWorld.setBlock, work fine.

This issue van easily be reproduced on Bukkit by creating a BO3 with a large overhang. I haven't tested on Forge yet.

This issue was originally reported here by Q2Lummox.

Tomorrow I'll continue debugging this.