In my experience: Amazon automatically discounts some books, a certain time after their release. I've published several through their subsidiary CreateSpace, and the two that sold more than negligible amounts were discount the same ~28%. One eventually went back to my 'retail' and the other stayed discounted.

Again in my experience, Amazon's discounts do not effect the author's take. At least in CreateSpace, the author's royalty is based on the retail price the author sets.