Why do my shins hurt?

I am by no means a runner. I have never liked running and have never been good at it either. When I was younger I would sometimes hyperventilate when I had to run a mile for gym class. I tried running for exercise this past year at college and I succeeded in jogging about 1.5 miles so I decided to try it at home too. Due to my low endurance, I could only run for a short period of time. However, after about a week of short nightly jogs, my shins started to really hurt. I thought it was maybe shin splints so I continued to run a short distance every day. The pain got worse so I went to a sports medicie doctor and I got MRI's from which she determined that I almost had stress fractures. I was given a boot for one leg and an aircast for the other and was told that about two weeks off from impact sports would be sufficient time to heal. I didn't run for a few months and when I did again at school I was fine. My shins hurt a little when I was wearing my old sneakers but I was fine with my new one recommended by the doctor. Now I am home and it has been about six months since my initial problem and again after about a week of very short runs my legs are hurting again. I really didn't run often at school and at home I run less than a mile and it causes pain. I would think that people who run more often or " too much" would have this problem, not someone who just started trying to run for fitness. Why do my legs keep hurting and how can I fix/ prevent this?