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I had a similar problem with clicking in my right ankle about 2 years back. It turns out that I had a bone in there called the Os Trigonum, which is usually present in around 5 - 15% of people. This turned out to be the cause of the clicking, as the bone rubbed against ligaments / tissues in the ankle.
My major problem came when my Os trigonum snapped off leaving bone floating around in my ankle. I was able to keep playing sport, but it got to the stage where I could hardly walk the next day.
I guess the main point is that if you know you've got a problem with your ankle, go and get it checked. The longer you leave it, the more damage you may do.
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