Something wrong using timer to capture pulses

I config the a WTIMER as  two split timer for event capture. The two signal input are nearly same. But one of the two timers is always later to match the same match value. And the load value of the two timer is the same. All I've figured out is that one of the timer work normally while the other one went wrong when the value is close to the match value. And I wonder why. Here's the code. I am using lm4f120.

#include <stdint.h>
#include <stdbool.h>
#include "inc/hw_memmap.h"
#include "inc/hw_types.h"
#include "driverlib/gpio.h"
#include "driverlib/sysctl.h"
#include "driverlib/pin_map.h"
#include "utils/uartstdio.h"
#include "driverlib/pwm.h"
#include "driverlib/timer.h"
#include "inc/hw_ints.h"
#include "driverlib/interrupt.h"

void right(void)
{
	TimerIntClear(WTIMER1_BASE, TIMER_CAPA_MATCH);//clear the interrupt
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_7, 0);
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_6, 0);
	UARTprintf("\nhello world, left\n");
}
void left(void)
{
	TimerIntClear(WTIMER1_BASE, TIMER_CAPB_MATCH);//clear the interrupt
	GPIOPinWrite(GPIO_PORTE_BASE, GPIO_PIN_5, 0);
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_5, 0);
	UARTprintf("\nhello world, right\n");
}

//*****************************************************************************
//To init the motor's pins, start to output after the func been called 
//*****************************************************************************
void ACMotorInit(void)
{
	//Set the GPIOs
	SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOA);
	SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOB);
	SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOE);
	SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOF);

	GPIOPinTypeGPIOOutput(GPIO_PORTE_BASE, GPIO_PIN_5);
	GPIOPinTypeGPIOOutput(GPIO_PORTA_BASE, GPIO_PIN_5);
	GPIOPinTypeGPIOOutput(GPIO_PORTA_BASE, GPIO_PIN_6);
	GPIOPinTypeGPIOOutput(GPIO_PORTA_BASE, GPIO_PIN_7);

	//The pwm pin
	//Config PB3 as T3CCP1
	GPIOPinConfigure(GPIO_PB3_T3CCP1);
	GPIOPinTypeTimer(GPIO_PORTB_BASE, GPIO_PIN_3);
	//Config PB2 as T3CCP0
	GPIOPinConfigure(GPIO_PB2_T3CCP0);
	GPIOPinTypeTimer(GPIO_PORTB_BASE, GPIO_PIN_2);
	//Config the timer
	SysCtlPeripheralEnable(SYSCTL_PERIPH_TIMER3);
	TimerConfigure(TIMER3_BASE, TIMER_CFG_SPLIT_PAIR | TIMER_CFG_A_PWM | TIMER_CFG_B_PWM);
	TimerLoadSet(TIMER3_BASE, TIMER_B, 60000);
	TimerMatchSet(TIMER3_BASE, TIMER_B, 30000);
	TimerLoadSet(TIMER3_BASE, TIMER_A, 60000);
	TimerMatchSet(TIMER3_BASE, TIMER_A, 30000);
	TimerEnable(TIMER3_BASE, TIMER_B);
	TimerEnable(TIMER3_BASE, TIMER_A);

	//Timer counter
	//WTIMER1 PC6 PC7
	SysCtlPeripheralEnable(SYSCTL_PERIPH_WTIMER1);
	SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOC);

	//Config the timer
	TimerConfigure(WTIMER1_BASE, TIMER_CFG_SPLIT_PAIR | TIMER_CFG_A_CAP_COUNT 
			| TIMER_CFG_B_CAP_COUNT);
	//Config C6 as WT1CCP0
	GPIOPinConfigure(GPIO_PC6_WT1CCP0);
	GPIOPinTypeTimer(GPIO_PORTC_BASE, GPIO_PIN_6);
	//Config C7 as WT1CCP1
	GPIOPinConfigure(GPIO_PC7_WT1CCP1);
	GPIOPinTypeTimer(GPIO_PORTC_BASE, GPIO_PIN_7);

	//Event ctl
	TimerControlEvent(WTIMER1_BASE, TIMER_A, TIMER_EVENT_POS_EDGE);
	TimerControlEvent(WTIMER1_BASE, TIMER_B, TIMER_EVENT_POS_EDGE);
	//Load set
	//TimerLoadSet(WTIMER1_BASE, TIMER_A, 0);
	//TimerLoadSet(WTIMER1_BASE, TIMER_B, 0);
	//Match set
	TimerMatchSet(WTIMER1_BASE, TIMER_A, 1000);
	TimerMatchSet(WTIMER1_BASE, TIMER_B, 1000);

	//Timer int enable
	TimerIntRegister(WTIMER1_BASE, TIMER_A, right);
	TimerIntRegister(WTIMER1_BASE, TIMER_B, left);
	TimerIntEnable(WTIMER1_BASE, TIMER_CAPA_MATCH | TIMER_CAPB_MATCH);
	IntEnable(INT_WTIMER1A);
	IntEnable(INT_WTIMER1B);
	IntMasterEnable();
	//Timer enable
	//TimerEnable(WTIMER1_BASE, TIMER_A);
	//TimerEnable(WTIMER1_BASE, TIMER_B);
}

//*****************************************************************************
//The left wheel to rotate exact distance
//the uint of the distance is the number of pulse of the photogate
//dir=1 to go ahead
//TimerB->Left
//*****************************************************************************
void LeftRotate(uint8_t dir, uint32_t distance)
{
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_7, dir?(~GPIO_PIN_7):GPIO_PIN_7);
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_6, dir?GPIO_PIN_6:(~GPIO_PIN_6));
	TimerLoadSet(WTIMER1_BASE, TIMER_B, distance+1000);
	TimerEnable(WTIMER1_BASE, TIMER_B);
}

//*****************************************************************************
//The right wheel to rotate exact distance
//the uint of the distance is the number of pulse of the photogate
//dir=1 to go ahead
//TimerA->right
//*****************************************************************************
void RightRotate(uint8_t dir, uint32_t distance)
{
	GPIOPinWrite(GPIO_PORTE_BASE, GPIO_PIN_5, dir?GPIO_PIN_5:~GPIO_PIN_5);
	GPIOPinWrite(GPIO_PORTA_BASE, GPIO_PIN_5, dir?~GPIO_PIN_5:GPIO_PIN_5);
	TimerLoadSet(WTIMER1_BASE, TIMER_A, distance+1000);
	TimerEnable(WTIMER1_BASE, TIMER_A);
}

//*****************************************************************************
//To adjust the rotate speed
//the var speed ranges from 0 to 100
//*****************************************************************************
void SpeedAdj(uint32_t speed)
{
	TimerMatchSet(TIMER3_BASE, TIMER_B, speed*100);
}