Oh wow, the Debug control section has some real goodies, huh? CTRL+SHIFT+E shows you all of the prototypes in the game. That would've been useful all this time. o.O
The bug is an oversight in the old IR3 code, it excludes anything with "dry" or "dead" in the name. The fix is simple, but IR3 keeps a cache of encountered trees and doesn't update it until a version bump, so you're stuck with it on that world.
I happen to like IR3 being at "4.0.0" and it also makes it easier for users to update by overwriting the file. Or I could swallow my pride and just do it, but it's only for a mod compatibility issue...
EDIT: Or I could cheat with a remote interface! In 0.5.1 you'll be able to run this to clean out the tree cache:
/c remote.call("ir3patchset", "clearTreeCache")