I have the exact same thing. Did you ever have an inversion sprain of the ankle? 90-95% of ankle sprains are eversion sprains (rolled out), but occasionally you have an inversion sprain (rolling in).
From what I understand from my doctor, when that happens, the ligament tends to pull off a piece of bone. That piece of bone will then settle and scar tissue will develop around it. It's then a crapshoot as to whether it will settle somewhere that will cause pain or not. If it does, you may need PT or surgery. If not, it will often make a clicking noise.
I had an inversion sprain five summers ago, and worst of all didn't rest up and ice enough. I now have a clicking in my left ankle every few steps, especially if I have been sitting for a while. It also clicks when I rotate it. I don't have any pain, however, so the doctors have said to leave well enough alone. Five years later I'm still doing moderately high mileage on it with no problems other than weirding out some of my training partners.