Instep/ankle pain after running

I've only noticed this recently and it's worrying me. I'm finding that after my runs (during which I feel fine, by the way...the problem doesn't happen until I stop and I've relaxed for a few hours), I'm having a shooting, almost grinding-type pain on the top of my foot near my instep. I think it might almost be at the junction of my foot and the front of my ankle. I don't know what tendons or ligaments are there, but I feel like it's at my talus. The wierd thing is that I only notice it when I point my toes. I also occasionally feel it when I push off excessively while walking, such as when I'm climbing stairs.

I'm not inclined to stop or take a break from running because it doesn't actually bother me while I run...but could this just be a strain or tendonitis or something similar? Could it be related to my fallen arches? I'm not really sure at what point I should see a doctor about something like this...