I'm having an issue with the pin drive when using peripherals such as TWI or UART. What happens is that it doesn't sink/source full voltage, see attached screen shots. It is like there is two levels.
The MCU is a AVR32DA28. Ignore the absolut voltage levels since I'm using series resistors.
First screen shot is of TWI SCL, where a few clocks have the correct voltage swing while the others don't sink enough. The behaviour is repeatable, always the same clocks which sink properly. The SDA never does the full swing. The second screen shot is of USART signal, where this middle step can also been seen but all the swings go the full way, so not a big issue but might be related.
The TWI hardware signal chain is as follows:
MCU -> series resistor -> oscilloscope probe -> +5V pull up -> TWI slave.
The TWI salve is known good.
any ideas what can be causing this?