Thank you for you answers.
stutyr - My road shoes are really old, so it could have lost cushioning, and I will buy a new pair soon. But the other one is new. It is a Solomon XA Pro 3D Ultra. I had a really painful race in this one back in may at the Three Forts Challange. Maybe I rather tend to land on my fore sole and this could cause the pain? I assume there are special shoes for this.
Runners Therapist - Yes, it is the ball of the foot. The whole ball gets sensitive and I have to carefully watch every single step to avoid pebbles and sharp edges. So far it always appeared after 13miles. I have never stoped because of this. Usually it subsides 20minutes after it appears while still runing.