Mine have hurt like that my whole life. I went to a knee doctor in high school who found out my hamstrings were tighter than normal. He said my quads were having to work extra hard during running and jumping, and it put a lot of pressure on my knees, shins, lower legs. I did somewhat have a tolerance for it, but now after years of not playing basketball and running, it hurts like hell when I try to run for extended periods. The more I stretch my legs before running, the more the pain is reduced. So, my advice is make sure you stretch very well before running.
And I have also gained a lot of weight since high school (60lbs).