It could very well possibly be the shoes you run in. If that's not the case, then you could have sprained it while running (over usage could cause mild sprains, then re-usage can sprain it worse).
I have had numerous ankle injuries in the past. I suffered through them when I first started running, as what your case could be. The best way I found to deal with it was to take a few days off the hardcore running, and just do light jogs maybe 2 times a week. Every second day, I went to the gym and did ankle strengthening exercises, along with the various supporting muscle workouts as well (i.e.: calf related exercises).
The best way I found to strengthen the ankles was to place a 35 pound plate on the floor and put your foot (say its your right foot for sake of example) right beside it so that the plate is on the outside of your foot. With your heel always connecting with the floor, try to push the plate as far as possible away from the starting position. Do this about 10 times, then do the same with the inside of your foot. Do for both feet. If it gets too easy, try increasing to a 45 pound plate, or if too hard, try downgrading.
Do this about 3 times a week, for the 2 weeks you have left, along with some running, but make sure you have a few rest days so your muscles can rebuild.
If it hurts too much after the workouts, just RICE it (rest, ice, compress, elevate) and all should go well.
I hope this helps, as I know the pain you feel. Those ankles sure are stubborn, but once you know how to deal with them, you shouldn't have much of a problem.
Cheers, and best of luck.
