Check out this article on shin splints in case this seems like the problem you might be experiencing: www.sparkpeople.com/resource/fitness_artic
I would say if the pain persists or gets worse, you should get it checked out by your doctor. The good news is that when it comes to weight loss, the majority of your progress comes from diet, not exercise. So even if you can't exercise as much as you'd like, you can still lose weight consistently if you're tracking all of your food and staying in your recommended calorie and nutrient ranges.
Hope that helps,