Not only did Apple’s (AAPL) iPad dominate with 88.3% of sales made on tablets, but the Kindle Fire’s miserable share (2.4%) was even smaller than Barnes & Noble’s (BKS) Nook (3.1%).

The picture was, if possible, even more bleak in a Monetate report that showed third quarter sales on the Kindle Fire falling from 2.18% in Q2 to 2.06% in Q3.

Given that Amazon sells its Kindle device at or below cost, it looked to the world like CEO Jeff Bezos’ words — “We want to make money when people use our devices, not when they buy our devices” — would come back to bite him.

But as Amazon PR was anxious to tell anyone who would listen, there was a problem with the data in those reports. Monetate readily admitted that it wasn’t counting sales made inside Amazon’s own store — where, presumably, most of the Kindle Fire shopping traffic is directed. IBM declined to say whether or not Amazon store sales were measured in its data, citing the confidentiality of its clients.

Making matters worse, Kindle Fires —  like all Google (GOOG) Android devices — often switch between desktop and mobile modes, depending on the site they are visiting. In desktop mode, a Kindle might be mistaken by a website’s analytics for a PC rather than a tablet.

The chart above shows how Chitika’s analysis of monthly tablet impressions changed after Amazon started working with the company to sort out data from the various user agents employed by its Silk browser. In October, the Kindle Fire was in ninth place with 0.59%. In November, under Amazon’s guidance, it moved to first, with 4.05%.

Note that those percentages are average tablet impressions per 100 iPads. If the iPad were included in either chart, the bar representing its impressions would tower over the others, too tall to fit on the screen.

UPDATE: If Bezos was losing money on Kindle sales before the holidays, he’s losing even more now. On Monday, Amazon cut the price of the 8.9-inch Kindle Fire HD from $299 to $249.