Temperature. The highest the temperature while fermenting, the sourer it becomes.
Sourness of added yogurt. If you add sour yogurt to the warm milk, the produced yogurt will be sour too.
Why isn't it sour all over?
Maybe your yogurt maker is warming the milk on the top and not much in the bottom and that might explain the difference in sourness. Try wrapping it in a thick, warm blanket (the one that you use in your bed for very cold winter nights) right after mixing the yogurt, in order to keep it evenly warm until it thickens (no machine needed).
Some more tips:
The milk should be 38-43° Celcius when you add the yogurt, NOT higher.
12h might be too much. Try leaving it for about 5 hours or overnight. If it hasn't thickened till then, just leave it in the blanket until it does (that's what have worked for me so far).