Layers in Ice cream base after ageing

I used this recipe to make a philly vanilla base. When I woke up in the morning it had separate layers. I mixed it up using a had blender. But again after a few hours same happened. Am I doing wrong? Can anyone please suggest what I can do? I want sugar lower for add ins. I usually cook the base to 185F then lower the flame to minimum and then cook for 2 more minutes and then take it off flame. I use pasturized A2 milk.