Even when that option is enavked, different maps use diffrent hitsounds from your skin, if thats what you mean. Not all maps have the same hitsounding, and when you disable map hitsounds, it uses the hitsound of the same filename from your skin instead.
Otherwise if thats not what you mean, make sure beatmap hitsounds arent enabled on each specific map youre playing, you can check this in the menu ay thw bottom of the screen before a map starts