TM4C123GH6PM: Pulse Capture Issues

Hello, 

I am tring to properly capture the up-time for a 333Hz pulse. The pulse is a PPM signal from a RC tx, so the duty cycle of the input is adjustable. I am having a problem: when I drop the duty cycle of the input the values for the capture just from the period of time low of the signal, to the period of time high on the signal. I think this is happening because the timer I am using is rolling over and making the data useless. Any insight would be very helpful. Thank you.

#define PART_TMC123GH6PM

#include <stdint.h> // Variable definitions for the C99 standard.
#include <stdio.h> // Input and output facilities for the C99 standard.
#include <stdbool.h> // Boolean definitions for the C99 standard.
#include "inc/hw_ints.h"
#include "inc/hw_types.h"
#include "driverlib/debug.h"
#include "driverlib/rom.h"
#include "driverlib/sysctl.h"
#include "driverlib/pwm.h"
#include "driverlib/sysctl.h" // Definitions and macros for System Control API of DriverLib.
#include "driverlib/interrupt.h" // Defines and macros for NVIC Controller API of DriverLib.
#include "driverlib/gpio.h" // Definitions and macros for GPIO API of DriverLib.
#include "driverlib/timer.h" // Defines and macros for Timer API of DriverLib.
#include "driverlib/pin_map.h" //Mapping of peripherals to pins for all parts.
#include "driverlib/adc.h" // Definitions for ADC API of DriverLib.
#include "driverlib/fpu.h" // Prototypes for the FPU manipulation routines.
#include "inc/tm4c123gh6pm.h" // Definitions for the interrupt and register assignments.
#include "inc/hw_memmap.h" // Memory map definitions of the Tiva C Series device.
#include "inc/hw_types.h" // Definitions of common types and macros.



volatile int intFlag=0;
volatile int widthFlag=0;
volatile unsigned int posEdge=0;
volatile unsigned int negEdge=0;
volatile unsigned int pulseWidth=0;
volatile unsigned int valueArray[10];
volatile unsigned int i=0;
volatile unsigned int posAverage=0;
volatile unsigned int divVar=10;
double x=0;
double checkVar=0;

void TIMER_Initialize(void)
{
// Enables timer 1
    SysCtlPeripheralEnable(SYSCTL_PERIPH_TIMER1);
    SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOB);
// PB5 pin configured with timer 1
    GPIOPinConfigure(GPIO_PB5_T1CCP1);
// Timer type set
    GPIOPinTypeTimer(GPIO_PORTB_BASE, GPIO_PIN_5);
// Configure timer to edge time capture
    TimerConfigure(TIMER1_BASE, TIMER_CFG_SPLIT_PAIR | TIMER_CFG_B_CAP_TIME_UP);
// Event set to both pulse edges
    TimerControlEvent(TIMER1_BASE, TIMER_B, TIMER_EVENT_BOTH_EDGES);
    TimerPrescaleSet(TIMER1_BASE, TIMER_B, 255);
// Configure timer 1b interrupts
    IntEnable(INT_TIMER1B);
// Enable timer interrupts
    TimerIntEnable(TIMER1_BASE, TIMER_CAPB_EVENT);
    // Enables processor interrupts
    IntMasterEnable();
// Enables the timers
    TimerEnable(TIMER1_BASE, TIMER_B);

}

int main(void)
 {
    SysCtlClockSet(
          SYSCTL_SYSDIV_64 | SYSCTL_USE_PLL | SYSCTL_OSC_MAIN
                  |SYSCTL_XTAL_16MHZ);
    TIMER_Initialize();

    while (1)
    {
      //checkVar = TimerLoadGet(TIMER1_BASE, TIMER_B);
      //TimerEnable(TIMER1_BASE, TIMER_B);

    }
}

void Timer1IntHandler(void)
{
   TimerIntClear(TIMER1_BASE, TIMER_CAPB_EVENT);
     if (intFlag==0)
    {
    posEdge=TimerValueGet(TIMER1_BASE, TIMER_B);
    intFlag=1;
    widthFlag=0;
    }
    else
    {
    negEdge=TimerValueGet(TIMER1_BASE, TIMER_B);
    intFlag=0;
    widthFlag=1;
    }
    if ((widthFlag==1)&&(negEdge>posEdge))
        {
            pulseWidth = (negEdge - posEdge);
            valueArray[i]=pulseWidth;
            x+=valueArray[i];
            i++;
        }
    if (i==10)
    {checkVar=TimerValueGet (TIMER1_BASE, TIMER_B);
        i=0;
        posAverage=(x/divVar);
        x=0;
        divVar=10;
        posEdge=0;
        negEdge=0;
       // TimerLoadSet(TIMER1_BASE, TIMER_B, 20000);
    }

}