you do not show any code, you use an ancient version. i would advise to update.
then it is also good to know that config port/pin also sets the DDR register.
when you make the port register high, it will create a pull up in normal avr chips but not in xmega.
xmega has a special register for this. so it is amazing that it works for you.
you need to use the pinctrl register to set the pin in pullup mode. config xpin does this on a pin or group.
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