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When you did the clean install, did you delete the nUI.lua file in your WTF folder? If not, then the clean install did nothing to reset your configuration settings for nUI.
That said, have you used the '/nui hud cdmin {n}' command at any time? It may be that your minimum cooldown setting is greater than the cooldown period for the spells in question. You might want to consider exiting WoW and going to your [ World of Warcraft ] folder then renaming [WTF] to [WTF.saved] then logging back in.
I play an affliction lock and haven't seen any cooldown issues on him... which is not to say there aren't any.
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