This is because blood sugar levels become very low when you haven't eaten in awhile. Your body doesn't like this and will crave whatever it thinks will raise it's blood sugar levels the quickest. That's why you were craving refined sugar; because it spikes your blood sugar much higher than any other food, even refined flour.

Diet has an effect on everyone. It's how the body functions. But it takes more than 45 hours. Also, your cysts may be an allergic reaction. I get cysts from citrus. If I hadn't figured that out first, I too would have thought my 'clean' diet had no effect on my acne because I would probably have still consumed some citrus.

Also, depends on what you mean by 'clean.' What you want is a blood sugar stabilizing, anti-inflammatory and nutrient dense diet.