Program skipping subroutines and infinite loops sometimes.

Hi, I made a program that reads data from an MPU6050 and also has a timer interrupt to move some motors.

However some of my Calculation functions are never being called and even when I step through the program it just goes right past them.

I am also experiencing infinite loops in for statements that are larger than 1000;

Does a interrupt subroutine destroy my local variable stack and it get's reinitialized when it returns?

volatile unsigned int count = 0;
	volatile unsigned int count2 = 0;


	P8OUT ^= BIT2;
	P4OUT ^= BIT0;

	while(count<1000){
	count++;
	P8OUT ^= BIT1;
	P4OUT ^= BIT3;
	__delay_cycles(100);
	P8OUT ^= BIT1;
	P4OUT ^= BIT3;
	__delay_cycles(100);

	}

	P8OUT ^= BIT2;
	P4OUT ^= BIT0;
	while(count2 < 1000)
	{
		P8OUT ^= BIT1;
		P4OUT ^= BIT3;
		__delay_cycles(1000);
		P8OUT ^= BIT1;
		P4OUT ^= BIT3;
		__delay_cycles(1000);
		count2 = count2 + 1;
	}

}

This is another bizarre area in my code that I am unsure of what is happening

void DERIVATIVE_CALCX();
void INTEGRAL_CALCX();
void positionCalc();

are all being skipped.

void BYTES_TO_INT()
{

	if(LOCATION_LOOP ==20)
	{
		LOCATION_LOOP = 0;
	}

	IMU_DATA[LOCATION_LOOP].xAccel = RXData[0] << 8 | RXData[1];
	IMU_DATA[LOCATION_LOOP].yAccel = RXData[2] << 8 | RXData[3];
	IMU_DATA[LOCATION_LOOP].zAccel = RXData[4] << 8 | RXData[5];
	IMU_DATA[LOCATION_LOOP].xRot = RXData[6] << 8 | RXData[7];
	IMU_DATA[LOCATION_LOOP].yRot = RXData[8] << 8 | RXData[9];
	IMU_DATA[LOCATION_LOOP].zRot = RXData[10] << 8 | RXData[11];

	void DERIVATIVE_CALCX();
	void INTEGRAL_CALCX();
	void positionCalc();

	int i = 0;

	LOCATION_LOOP ++;

	for(i = 0;i<14;i++);
	{
		RXData[i] = 0;
	}
}