TM4C123AE6PM: Wave generator timing issue with TM4C123, SSI

Hello everyone, 

I need advice regarding some software design. Here is the quick explanation, I have some DAC which generates some analog signal as a response to some input square signal. It generates some small output wave which starts at rising edge and ends at falling edge of the input signal. Communication between MCU and DAC is via SSI interface. I set up GPIO interrupt on the input signal so when rising or falling edge occurs, the system is informed. On rising edge, I start to send via SSI values to the DAC. Sending is done within timer interrupt which runs at 250kHz. The frequency of input signal is max 100Hz, and at that frequency error is not too visible, but at a higher frequency, I see a bigger difference between rising edge and the start of the output wave. Output wave is delayed some time behind input square signal. Here are chunks of code, so maybe if You have some advice of what I am doing wrong, maybe I should generate a signal in the main loop, and not in the timer interrupt? 

void portB_ISR(void)
{
	if(GPIOIntStatus(INPUT_SQUARE_PORT, false)&INPUT_SQUARE_PIN){
		if(GPIOPinRead(INPUT_SQUARE_PORT, INPUT_SQUARE_PIN))//edge was rissing
		{
			flag_falling=1;
			flag_rising=0;
			ui32_timer_cnt=0;
		}
		else //edge was falling
		{
			  flag_rising=1;
			flag_falling=0;
			ui32_outval=PEEK_OUTPUT_VAL;
		}
		GPIOIntClear(INPUT_SQUARE_PORT,INPUT_SQUARE_PIN);
	}
}

void Timer1_ISR(void)
{
	TimerIntClear(TIMER1_BASE, TIMER_TIMA_TIMEOUT);

	if(flag_ssi_fifo)
	{
		SSIEnable(SSI0_BASE);

		if(flag_TDI){
			flag_count_pickup=0;
			//falling edge in input signal 
			if(flag_falling)
			{
				if(ui32_timer_cnt<BOOST_COUNT){	
						pui32DataTx[0]=ui32_outval;
						SSIDataPut(SSI0_BASE, pui32DataTx[0]);
					ui32_outval=ui32_outval+85;
				}
				else	
				{
					if(ui32_outval>540)
						ui32_outval=ui32_outval-50;
					else if(ui32_outval>416)
						ui32_outval=ui32_outval-10;
					else
					{
						if(ui32_outval==416)
							ui32_outval=370;
						else
							ui32_outval=416;
					}
						pui32DataTx[0]=ui32_outval;//pui32SqrLkp_256[angle];
						SSIDataPut(SSI0_BASE, pui32DataTx[0]);
				}
			}
			//rising edge in input signal -> turn off output signal
			else if(flag_rising)
			{

				ui32_outval=0;
pui32DataTx[0]=ui32_outval;
					SSIDataPut(SSI0_BASE, pui32DataTx[0]);			}
		}
	}
	if(flag_count_pickup)
	{
		ui32_pickup_cnt++;
	}
	ui32_timer_cnt++;
	if(SSIBusy(SSI0_BASE))
		flag_ssi_fifo=0;
	else
		flag_ssi_fifo=1;
}

void SSI_Configuration()
{
	SysCtlPeripheralEnable(SYSCTL_PERIPH_SSI0); 
	GPIOPinConfigure(GPIO_PA2_SSI0CLK);
	GPIOPinConfigure(GPIO_PA3_SSI0FSS);
	//GPIOPinConfigure(GPIO_PA4_SSI0RX);  //RX is not used
	GPIOPinConfigure(GPIO_PA5_SSI0TX);
	GPIOPinTypeSSI(GPIO_PORTA_BASE, GPIO_PIN_5 | GPIO_PIN_3 | GPIO_PIN_2);
	SSIConfigSetExpClk(SSI0_BASE, SysCtlClockGet(), SSI_FRF_MOTO_MODE_0, SSI_MODE_MASTER, 16000000, 16);
	SSIEnable(SSI0_BASE);
}