Проблема решена, все дело оказалось в маленьком различии USART A3 и A3U, ну и невнимательности конечно...
XMEGA A MANUAL
Цитата
21.6.2 Disabling the Transmitter
A disabling of the Transmitter will not become effective until ongoing and pending transmissionsare completed, i.e. when
the Transmit Shift Register and Transmit Buffer Register do not contain data to be transmitted. When Transmitter is
disabled it will no longer override the TxDn pin and the pin direction is set as input.
XMEGA AU MANUAL
Цитата
23.6.2 Disabling the Transmitter
A disabling of the transmitter will not become effective until ongoing and pending transmissions are completed; i.e., when
the transmit shift register and transmit buffer register do not contain data to be transmitted. When the transmitter is
disabled, it will no longer override the TxDn pin, and the pin direction is set as input automatically by hardware, even if it
was configured as output by the user.
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