Atmel ASF SAM4E UART0 Firing Erratically

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.