UG526 (v1.5), Figure 1-2, shows Number 6 as the USB JTAG connector, and shows Number 12 as the USB UART connector. These have been incorrectly swapped.
Looking at Figure 1-2, Number 6 is in fact the USB UART port, while Number 12 is the USB JTAG connector. This is correctly labeled on the silkscreen of the board and in the schematic, and there is no Hardware issue associated with this.
This has been corrected in UG526 (v1.6), July 18, 2011.
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