I just submitted this bug report regarding missing code in board_init.c for the XMEGA-A1U Xplained Pro that configures USART Rx/Tx pins. Code only exists for USARTE0, the one that connects to the EDBG. There is no code for the three USARTs that appear on the Extension Headers.
I made changes to two files: board_init.c and conf_board.h
EDIT: put [BUG] in the title.