Can you do me a favor please and try to reproduce that problem then post me some screen shots... I need to see it to see what's going on.
What kind of system are you playing on? Video card? Were your action bar buttons the only thing fading, or was everything fading?
nUI does not fade buttons or action bars except when they are unusable... maybe that's what was happening is WoW was getting confused on what was and was not usable? You might try the '/nui bar dimming' option to turn that off and see if that fixes it.
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