CCS/MSP430G2553: Trying to detect the half cycle of a sine wave

Tool/software: Code Composer Studio

I am still fairly new to MSP430 and CCS and I'm currently working on trying to determine how long it takes a sine wave to hit 0 twice or the half cycle of the wave. The wave is generated by a function generator at 1KHz and is offset so there is no negative component.  The ADC works fine and I can detect when the sine wave hit 0. I also have a TimerA interrupt that gets activated every 0.0001 secs at which point interuCounter is incremented and is how I keep track of time between the two 0's of the wave. However when I try to count the time in between those two instances of voltage = 0 I keep getting "difference=1" no mater what I make the frequency. With 1KHz I should expect 10. Am I implementing the timer wrong? Or is something else missing that I'm overlooking? 

#include "msp430g2553.h"
#include "intrinsics.h"
int voltage=0;
int flag1=1;
int flag2=0;
int count=0;
int preCount=0;
int difference=0;
int flag3=0;
int interuCounter;
int sawZero;
void main(void)
{
   WDTCTL = WDTPW  + WDTHOLD;    // stop WDT
   DCOCTL = 0;
   BCSCTL1 = CALBC1_1MHZ;
   DCOCTL = CALDCO_1MHZ;


   ////////////////////////////////////////////////////////
      //TimerA setup
      TA0CCR0 |= 100; //count up to 100 (1/1MHz*100 = 0.0001 sec interrupt)
      TA0CCTL0 |= CCIE;
      TA0CTL |= TASSEL_2 + MC_1;//SMCLK clock, count up mode

     // _BIS_SR(LPM0_bits + GIE); // Sleep in LPM0 with interrupts enabled

   //////////////////////////////////////////////////////////////////////////////////////////


   // ADC configuration,V+ref=3V,V-ref=0V,Channel=A0

   ADC10CTL0  = ADC10ON + ADC10IE; // Vref Vr+=3v,Vr-=VSS,
                     // S&Htime = 4 X ADCCLK,ADC10 on,ADC interrupts enabled
   ADC10CTL1  = ADC10DIV_7; // INCH =0000->A0,ADCCLK src = ADC10CLK,
                            // ADCCLK/8,Single Channel Single Conversion
   ADC10AE0   = INCH_0;     // channel A0

   ADC10CTL0 |= ENC + ADC10SC; // Start Conversion

   _BIS_SR(LPM0_bits + GIE); // Sleep in LPM0 with interrupts enabled
}

/***************************************************************************/
/*                 interrupt vectors for MSP430                            */
/***************************************************************************/

#pragma vector = ADC10_VECTOR
__interrupt void adc10_interrupt(void)
{
  ADC10CTL0 |= ENC + ADC10SC;  // Start Conversion again
  voltage = ADC10MEM;//voltage will be whatever ADC reads
  P1DIR |= BIT6;
  P1OUT &= ~BIT6;


  }



#pragma vector=TIMER0_A0_VECTOR     // Timer0 A0 interrupt service routine
   __interrupt void Timer0_A0 (void) {

   interuCounter++;//increment every 0.0001 secs

   if(flag2==1)//Enter third if statment if I see  voltage=0 again
     {
        flag3=1;
    }
    if(voltage==0 && flag1==1)
     {
        preCount =interuCounter; //count when I first saw voltage=0
        flag1=0; //Don't enter this statement again unless I've already seen 0 twice
        flag2=1;//Enter third if statment if I see voltage=0 again
     }
    if(voltage==0 && flag3==1)
        {

           flag1=1;//RESET
           flag2=0;//RESET
           flag3=0;//RESET
           count=interuCounter;//count at second instance of voltage=0
           difference = count-preCount; //Difference between first instance an second instance of 0
           P1OUT |= BIT6;


        }


}