Saplings pick the highest block to grow on, instead of the block they are placed on causing them to be unable to grow unless the highest block is either dirt(or another block trees can grow on) or if the block is the highest already.
This video shows the process I used: https://www.youtube.com/watch?v=8RwkzX5I9Bo

This applies to both bonemeal and natural growth.

I believe this has been in previous snapshots but I have not checked.

Here is a screenshot showing the 5 different trees that grow wrong, 2x2 trees grow properly.