I agree, you need to make sure your shoes are not the problem.
Also are there any underlying conditions that might be causing the pain? I ask because I have sprained my left ankle 3 separate times since the first in 5th grade. This has caused that ankle to be a little bit stiffer and while I am running, if I land on it wrong, I tend to twist it causing pain.
You have to listen to what your body is telling you and if the pain do not improve, then you need to check with your doctor. You should never force yourself to run if it hurts.