Hi,
I have the same problem with receiving characters via programming port. To solve the problem, did you just put the code (mentioned below) for this to work or is it also required to use the pull-up resistors along with the macros (also mentioned below)? Besides, does this solution still requires the use of the 5V power connector?
Thanks in advance 
/* ------------------------------------------------------------------------ */
/* UARTÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â */
/* ------------------------------------------------------------------------ */
/*! UART pins (UTXD0 and URXD0) definitions, PA8,9. (labeled RX0->0 and TX0->1)*/
#define PINS_UARTÂ Â Â Â (PIO_PA8A_URXD | PIO_PA9A_UTXD)
#define PINS_UART_FLAGSÂ (PIO_PERIPH_A | PIO_PULLUP)
#define PINS_UART_MASK (PIO_PA8A_URXD | PIO_PA9A_UTXD)
#define PINS_UART_PIOÂ PIOA
#define PINS_UART_IDÂ ID_PIOA
#define PINS_UART_TYPE PIO_PERIPH_A
#define PINS_UART_ATTR PIO_PULLUP