In a minecraft 1.2.3 world, I have created an underground area for growing trees. The four dirt blocks you see (two on left) all can grow trees, but with the others, they never grow, even when using bone meal.
The vertical wall is six blocks high, and they all have two clear spaces beside them. The only thing is that the one dirt block you see closest is also just outside the opening of a straight and normal stairwell. Does that affect it too?