Hi XiangJun Rong,
Thanks for the reply,
I checked the line and got the issue, I had not configured the falling edge trigger option,
I enabled it and now both the line toggling and the input to the capture is matching.

Yellow line is the line toggled and the blue one is the ZCD input from the development board.
#define CAP_NUMB 0
#define TIMER2_PRESCALER 1
#define UPPER_LIMIT_32 0xFFFFFFFF
ui32_timerFreq = Chip_Clock_GetRate(CLK_MX_TIMER2);//Chip_Clock_GetSystemClockRate();//(PRESCALE_COUNT+1);
Chip_GPIO_Init(LPC_GPIO_PORT);
Chip_SCU_PinMux(0x6,1, MD_PLN_FAST, SCU_MODE_FUNC5);
LPC_GIMA->CAP0_IN[2][0]|= (2 << 4) ;//| (1 << 1);//0x20
Chip_SCU_PinMuxSet(0x02, 12,(SCU_MODE_INACT | SCU_MODE_INBUFF_EN | SCU_MODE_ZIF_DIS |SCU_MODE_FUNC0));
Chip_GPIO_SetPinState(LPC_GPIO_PORT,1,12,true);
Chip_GPIO_SetPinDIROutput(LPC_GPIO_PORT,1,12);
Chip_TIMER_Init(LPC_TIMER2);
Chip_RGU_TriggerReset(RGU_TIMER2_RST);
while (Chip_RGU_InReset(RGU_TIMER2_RST)) {}
Chip_TIMER_Reset(LPC_TIMER2);
// Chip_TIMER_TIMER_SetCountClockSrc(LPC_TIMER2, TIMER_CAPSRC_BOTH_CAPN, CAP_NUMB);
Chip_TIMER_PrescaleSet(LPC_TIMER2, TIMER2_PRESCALER);
Chip_TIMER_ClearCapture(LPC_TIMER2, CAP_NUMB );
Chip_TIMER_CaptureRisingEdgeEnable(LPC_TIMER2, CAP_NUMB);
Chip_TIMER_CaptureFallingEdgeEnable (LPC_TIMER2, CAP_NUMB );
Chip_TIMER_CaptureEnableInt(LPC_TIMER2,CAP_NUMB);
Chip_TIMER_SetMatch(LPC_TIMER2,0,0xFFFFFFFF);
Chip_TIMER_ResetOnMatchEnable(LPC_TIMER2,0);
NVIC_EnableIRQ(TIMER2_IRQn);
NVIC_ClearPendingIRQ(TIMER2_IRQn);
Chip_TIMER_Enable(LPC_TIMER2);
Also need to change the Prescaler to 1 and now I am running the at 100Mhz both controller and timer as well.
But there is one observation, if we consider the clock freq 100Mhz , then expected difference for complete cycle is around 200 counts but the difference observed is not as per the expectation.
see the below screen shot


It is not stable to 50Hz it is fluctuating between 49Hz to 50Hz. Here the variable "ui32_current_half_cycle_time" is just a difference between the current and previous capture value of timer 2. And as per the formula the value come around 20Mhz
channels[0].ui32_frequency = (uint32_t)(((uint64_t)ui32_timerFreq*(uint64_t)1000)/(uint64_t)channels[0].ui32_current_half_cycle_time);
Got the reason, changed the Prescaler to 0 from 1 and kept only Rising edge trigger. Now it is coming closer to the expected value.
Also attached the code which w.r.t Capture functionality for LPC4367 over OEM13088.
Please check w.r.t the configuration and the if there is any thing you find that need to be modified pls suggest.
Thanks
Gaurav More