It could just be the 2 mile and 3 mile runs. But it is common for a post-op body parts to have some discomfort and feel achy in the cold. Have you tried runs at that distance in warmer weather? How has your rehab been going/did it go? You are still only 1 year post-op, so some residual discomfort from the surgery during and after activity is to be expected.
Have you discussed this with your ortho?