Don't know if you'd call it a bug...in fact I really don't know what to call it. I had the same problem. And I had to restart from save sometime before entering Dragon's Eye. Unfortunately, it seems that (in my game at least) if you kill the wyvern before you find Mandal (and maybe do the ghosty stuff) then you can't find the root.
Sorry for the bad news... And trust me, I know how frustrating it is.
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