We recently moved our Minecraft server instance back to CraftBukkit so we can once again manage it with the wide variety of useful administrative plugins supported by the Bukkit community. Unfortunately, as with all development-quality software, CraftBukkit's recommended build for Minecraft v1.0.1 has a few problematic issues. Chiefly, if you've recently planted a tree farm, you'll notice that your saplings may have disappeared. This is due to a bug the tree growth detection code and has been fixed in the latest snapshot which we're currently running.
I apologize for the inconvenience.