Ever drop something (heavy) on your foot?
I dropped a few 1x6x8 pieces of Oak on my foot last June, and am still feeling pain to this day. Apparently, I had a hairline fracture in my first metatarsal bone that never healed properly. I'm unable to walk properly and keep exacerbating the injury, which totally sucks because it cuts into the biking.
Get an X-Ray to see if there is some mechanical damage to the bones.