When I reported on the story on Tuesday, I knew little more than that the negotiations had hit a snag. The original BI article didn't include any direct quotes, just unnamed sources, but it was later updated to include this statement from Amazon:
I can't comment on that rumor. I can say that we have offered Harper the same terms for a contract that Simon & Schuster, Hachette, and Macmillan have all recently agreed to.
I can also add that Publishers Lunch said that the contract negotiation had been going on for over a year.