From 1st March a new revision of the Associates Operating Agreement was put into place which aims to cut out people bumping their commission rates by promoting free eBooks. Here is the relevant text: As always make sure you are fully aware of the Operating Agreement: https://affiliate-program.amazon.com/gp/associates/help/operating/advertisingfees
Also, the number of free and paid Kindle books are separately shown at Miscellaneous Referrals page in your account