The caffeine brain fog has always been present with me, ever since I started taking it. Normally, caffeine clears brain fog, because it increases dopamine in the brain. I also don't feel that anxious with the caffeine, which makes me think that it isn't a lack of GABA either. It's just some sort of inflammatory response caused by the histamine, I believe.
I take caffeine once or twice a day (once in the morning and once at around 3 PM). That allows me to function without too much (at times, none at all) brain fog.