I created some custom trees and replaced all saplings like this in my forest-biome:
Sapling(Oak,Baum01,70,Baum02,100)
Sapling(Redwood,sapling_redwood,100)
Sapling(Birch,sapling_birch,100)
Sapling(SmallJungle,sapling_jungle,100)
Sapling(BigJungle,sapling_jungle,100)
Sapling(Acacia,sapling_acacia,100)
Sapling(DarkOak,sapling_darkoak,100)
Sapling(HugeRedwood,sapling_redwood,100)

Like you can see only oak-saplings spawn my 2 test-trees, all other spawn a sapling so nothing happens. Problem: I spam for example some acacia-saplings with bone meal and then sometimes they changed into normal oak-saplings. I tested also with other types of saplings and also changed my trees to spawn from redwood-saplings but sometimes saplings changed into normal oak-saplings. Seems like the hole sapling-method has a little bug changing saplings to oak-type.

System: newest craftbukkit 1.8.3 (git-Bukkit-7d020a7) and TerrainControl (Jenkins #87) build but also noticed under older 1.8-builds