I always associate achiness with muscle weakness. I experience random achiness in my ankles and feet, as well.
I think it's kind of a misnomer in exercises, such as running -where you are using
many different muscles- that
all of the muscles that need to be strong to do the exercise well,
are strong.
I have taken to using this fine exercise tool to help increase the strength in my ankles and feet. After I initially started using it (a couple weeks ago), I was surprised at how many muscles in my feet and ankles were sore the next day. I mean, I run trails for pete's sake. You'd think with all that variable terrain that there would not be a foot or ankle muscle untouched. Anyway, now that I've started using it, I think that all runners should use it.
http://www.amazon.com/Altus-Athletic-Core-Balance-Disc/dp/B001FB5ZEO/ref=sr_1_1?ie=UTF8&qid=1339616557&sr=8-1&keywords=balance disc