I'm having a similar problem with my salomon f20. My Achilles tendon is getting rubbed raw (really only on my back foot). I thought the prob would disappear after the break-in period, but 6 full days in them and it's just as bad as day 1. For now, the solution is to put one of those big square bandages on my tendon area to pad/buffer the chaffing. The boots, otherwise, fit perfect, so I'd rather buy more bandages and hope things naturally get better.
don't wait until your heels start hurting to put the pad on...do it before your first run