Regarding Atmel's labelling and quality control-
We designed a product using AT90USB1287 (has USB host and device).
We assembled 100 units and the USB host feature did not work on them.
After much fault finding, chasing of distributors and confusion we heard that Atmel had probably shipped a large (unknown) number of AT90USB1286 devices (no USB host feature) incorrectly marked up as AT90USB1287.
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Tim Mitchell