Yeah, others have reported this same problem. Killing the ancient wyvern ahead of time somehow prevents the root from appearing. It really is necessary to have Mandal show you the spot before you kill the critter.
However, if your last save is too far back, you can always use the cheat console to create the root and go on from there. I don't consider this cheating, since you're using it to overcome a flaw in the game.
Nightowl2
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