OK, cool. Sounds like it might be the joint line then. The rapid pumping of downhill is on the ankle a bit like the arm pump on the triceps. And at that time you body will be trying to fix you ankles to keep you connected to the bike. I think maybe some simple mobilizations of the ankle joint in different ranges of movement might do the trick. Try to get into your local sport's PT.

p.s. Haven't down much downhill, but my brother does a lot and is about to get a new Demo 7 or 8. Pretty cool for someone close to 40!