[Ereki]

That's not really my problem, I didn't explain it properly when a rune is energized RUNE_POWER_UPDATE fires twice as I said but it's only the first time isEnergized is true, the second time it's nil and it's that second that I thought put the alpha back. But I modified what you said to:

elseif event == "RUNE_POWER_UPDATE" and InCombatLockdown() and not UnitInVehicleControlSeat("player") then
	local runeIndex, isEnergize = ...
			
	if isEnergize == true then
		G["RuneButtonIndividual"..runeIndex]:SetAlpha(RHaic)
		lastAlpha = GetTime()
	elseif lastAlpha+1 < GetTime() then
		if GetRuneCooldown(1) > 0 then
			RuneButtonIndividual1:SetAlpha(RHaoc) else 
			RuneButtonIndividual1:SetAlpha(RHaic)
		end
		if GetRuneCooldown(2) > 0 then
			RuneButtonIndividual2:SetAlpha(RHaoc) else 
			RuneButtonIndividual2:SetAlpha(RHaic)
		end
		if GetRuneCooldown(3) > 0 then
			RuneButtonIndividual3:SetAlpha(RHaoc) else 
			RuneButtonIndividual3:SetAlpha(RHaic)
				end										--Cooldown fading	
		if GetRuneCooldown(4) > 0 then
			RuneButtonIndividual4:SetAlpha(RHaoc) else 
			RuneButtonIndividual4:SetAlpha(RHaic)
		end
		if GetRuneCooldown(5) > 0 then
			RuneButtonIndividual5:SetAlpha(RHaoc) else 
			RuneButtonIndividual5:SetAlpha(RHaic)
		end
		if GetRuneCooldown(6) > 0 then
			RuneButtonIndividual6:SetAlpha(RHaoc) else 
			RuneButtonIndividual6:SetAlpha(RHaic)
		end
	end

And it still won't change the alpha so I might have been completely wrong, this is the whole lua file: http://www.pastey.net/141593
And I need some help in figuring out what the hell is wrong 'cause I'm out of ideas.