My mother had an injury similar to that once. It was Plantars Fascitis(sp?). I would recommend looking into that.
I'm not a doctor, just a woman who deals with Chronic Pain and gives people my best guess. :)
I have plantars fasciitis and for me the pain is at night when I sleep it wakes me up. In the morning or when I walk it is ok, or somewhat painful. The pain is on the bottom of my foot at the heel just near the arch in the daytime and at night at the back of the heel when I am laying on my back. I bought some walking shoes for plantars fasciitis and they have running shoes at orthofeet.com. You need to stretch your achilles tendon basically too. It could potentially be a heel spur but they have to Xray it to confirm that.
hope this helps. Also, putting gel heels from Dr. scholes (spelling?) helps it to feel better but the shoes need arch support and firm midsection.