I think Xrystal hit the nail on the head... there's an issue in the action bar dealing with talent spec swapping with respect to cooldowns. nUI is, technically, ignorant of dual spec and leaves it all to the WoW engine... but that blows up the cooldown timers in some cases.
I'll be fixing it in nUI6 but likely not in nUI5 and it requires too much action bar recoding.
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