it's probably a general inflammation of the metatarsal joint. There's a lot of stuff going on on the metatarsal heads, and sometimes the tissue around it can get inflamed. However, it could also be a stress fracture. If it keeps getting worse, stop running immediately and cross-train.
take out the insoles from your shoes. Is there a bigger "divet" where that part of your forefoot is? If there is, it might just be a structural thing with your foot.
You can try cutting out a metatarsal pad for the bottom of your insole. Get some moleskin (or preferably, podiatrist's felt) and make a pad like this:
http://www.aafp.org/afp/20020601/2277_f7.jpg
But instead of the way it's pictured above, cut out a slot for the third metatarsal head 9the one that hurts). Stick it to the bottom of your insoles. You might need to stack two on top of each other to make it thick enough. This can help a lot by taking the pressure off of that area. The idea is not to completely divert pressure from it, but instead to spread it out evenly.