A - You really paint them? Well if it's any consolation this condition (medically labelled, subungual hematoma) is extremely common amongst all levels of runners. And in many cases it's simply inexpicable, seemingly defying all rational grounds for its occurrence. Sure, you'll hear explanations that this problem ususally results from repeated trauma of the toe against the toe box or tight-fitting shoes across the toe area.
However, it appears that in some cases the trauma or concussion that the feet absorb with the repeated impacts may be a sufficient trigger.
In any case, the nail root or nail plate has been dammaged, thereby resulting in some nail deformity. Consequently, all I can suggest is experimenting with different shoes and perhaps increasing the percentage of running on softer (i.e., grass, cinder) surfaces. You will have to be tougher than nails.....