Atmel ASF SAM4E UART0 Firing Erratically - c

Question

I'm attempting to set up UART communication with a GPS module but keep running into some communication error. The GPS sends a packet approximately once a second to the SAM4E16E micro, which should be trigger an interrupt and read in the data. I have two UARTS which are configured like this
conf_uart.h
#include "asf.h" //uart.h etc. included here
#define UART_SERIAL_BAUDRATE 4800
#define UART_SERIAL_CHANNEL_MODE UART_MR_CHMODE_NORMAL
#define UART_SERIAL_MODE UART_MR_PAR_NO
#define UART_SERIAL_STOP_BIT US_MR_NBSTOP_1_BIT
/* =============== UART0 =============== */
#define PINS_UART0 (PIO_PA9A_URXD0 | PIO_PA10A_UTXD0)
#define PINS_UART0_FLAGS (PIO_PERIPH_A | PIO_DEFAULT)
#define PINS_UART0_MASK (PIO_PA9A_URXD0 | PIO_PA9A_URXD0)
#define PINS_UART0_PIO PIOA
#define PINS_UART0_ID ID_PIOA
#define PINS_UART0_TYPE PIO_PERIPH_A
#define PINS_UART0_ATTR PIO_DEFAULT
/* =============== UART1 =============== */
#define PINS_UART1 (PIO_PB2A_URXD1 | PIO_PB3A_UTXD1)
#define PINS_UART1_FLAGS (PIO_PERIPH_A | PIO_DEFAULT)
#define PINS_UART1_MASK (PIO_PB2A_URXD1 | PIO_PB3A_UTXD1)
#define PINS_UART1_PIO PIOB
#define PINS_UART1_ID ID_PIOB
#define PINS_UART1_TYPE PIO_PERIPH_A
#define PINS_UART1_ATTR PIO_DEFAULT
conf_uart.c
#include "conf_uart.h"
void uart_custom_init_1(void) {
// set the pins to use the uart peripheral
pio_configure(PINS_UART1_PIO, PINS_UART1_TYPE, PINS_UART1_MASK, PINS_UART1_ATTR);
//enable the uart peripherial clock
pmc_enable_periph_clk(ID_UART1);
const sam_uart_opt_t uart1_settings =
{ sysclk_get_cpu_hz(), UART_SERIAL_BAUDRATE, UART_SERIAL_MODE };
uart_init(UART1,&uart1_settings); //Init UART1 and enable Rx and Tx
uart_enable_interrupt(UART1,UART_IER_RXRDY); //Interrupt reading ready
NVIC_EnableIRQ(UART1_IRQn);
}
uart_custom_init_0(void)
{
// 1. Enable UART peripheral clock
//2. Enable the required PIO's
pio_configure(PINS_UART0_PIO, PINS_UART0_TYPE, PINS_UART0_MASK, PINS_UART0_ATTR);
pmc_enable_periph_clk(ID_UART0);
// 3. call init
const sam_uart_opt_t uart0_settings =
{ sysclk_get_cpu_hz(), UART_SERIAL_BAUDRATE, UART_SERIAL_MODE };
uart_init(UART0,&uart0_settings); //Init UART1 and enable Rx and Tx
// read on interrupt
uart_enable_interrupt(UART0,UART_IER_RXRDY); //Interrupt reading ready
NVIC_EnableIRQ(UART0_IRQn);
}
void UART1_Handler() {
uint32_t dw_status = uart_get_status(UART1);
if(dw_status & UART_SR_RXRDY) {
uint8_t received_byte1;
uart_read(UART1, &received_byte);
read_buffer[read_buffer_index] = received_byte;
read_buffer_index++;
}
}
void UART0_Handler() {
uint32_t dw_status = uart_get_status(UART0);
if(dw_status & UART_SR_RXRDY)
{
uint8_t received_byte0;
uart_read(UART0, &received_byte);
read_buffer[read_buffer_index] = received_byte;
read_buffer_index++;
}
}
UART1 works perfectly. UART0 Only fires roughly once per packet, and is not even getting the first byte in the packet (should be 36, receives 16). As far as I can tell they are identical. The chip is working, I can see it transmitting on the scope. I'm basically fresh out of ideas.