I'm not a physical therapist, but a guy that used to get lots of shin splints (real sharp pains up and down both sides of the shins - hard to walk on). In other words I have no idea what is going on with you, nor should I pretend to know. But, I'll offer a possible solution. I do the following as part of my stretching routine to work the shin muscles and it works miracles for curing and then preventing my shin splints...
Get in the lunge position - one foot forward and one foot back, feet in line, forward knee bent 90 degrees, back knee just off the ground, upper body over the forward knee. Put one hand on the ground for balance and the other one your toes, applying light pressure. Now raise your toes up against the light pressure from your hand. 2-3 sets of 20-25 reps will strengthen the shin muscles and may clear up the problem. At least it has helped me with my minor problems.