Creating larger trees where branches appear, all the branch log blocks appear to lay on the side and do not maintain the vertical orientation that the trunk logs or the way a tree would spawn naturally do.

The tree brush directly accesses the tree generation API. So it is using the exact same algorithm that is used in default Minecraft.
That means this is a Minecraft (or maybe Bukkit) issue, not a problem with Sniper.

Sorry didn't realize vanilla MC had changed the way branches looked.