The only thing I noticed with mine a couple of times was when I tied the tops too tight for going uphill. I would notice a pull or irritation to my achilles tendon but relacing them slighter looser at the top solved it.
If course I would relace and tighten them pretty good for the descent.
I've had my charmoz's 4 years so relatively trouble free for me.
Although the trail was fairly level to the base, maybe it's possible I tied them too tight like this? But I never noticed a pull or irritation, it was more discomfort after the fact, and the next day.
I agree it is an overuse injury, as I had not done anything to that extent for several months prior. But when I first bought them, I only hiked for a mile or two to break them in, and then took them on the 5 day trip in the Rockies, and I didn't have any of the problems I have had now...
I don't know if it is a fit issue or not... again, the boots were fine when I first bought them.
I will look into insoles, as I need them for my Nepals...