MSP430 Timer A interrupt flags are wacko

If possible I'd suggest selecting a microcontroller that supports a counter operation using the timer inputs; rather than manually incrementing a counter inside an ISR (which at high frequencies quickly ends up saturating the microcontroller activity) you allow the hardware to handle the counting. At this point your code simply becomes a matter of waiting for your periodic interrupt then calculating the frequency.

To extend the range and make the frequency counter more generalised (removing the need for multiple ranges at the expense of a little more work for the MCU) you could use the following technique.

Select a periodic interrupt rate that allows for measurement accuracy at the highest input frequency; this should take into account your counter size (you need to select the timer period such that the timer counter will not overflow at the maximum input frequency). For this example I'll assume that the input counter value can be read from the variable "timer_input_ctr".

Include a variable for counting periodic interrupts (should be initialised to 0 at startup); for this example I'll refer to this variable as "isr_count". The interrupt period is contained in the constant "isr_period".

Your periodic interrupt should be implemented as (C pseudo-code):

void timer_isr()
{
  isr_count++;
  if (timer_input_ctr > 0)
  {
    frequency = timer_input_ctr / (isr_count * isr_period).
    timer_input_ctr = 0;
    isr_count = 0;
  }
}

Obviously this rough example relies on some floating point math that may not be compatible for low-end microcontrollers, there are techniques to overcome this but they are outside of the scope of this answer.

Not sure exactly which series MSP you're using so you'll have to look up the specifics. But the basic premise should apply across the board I think.

The following example is from the file msp430g2xx1_ta_03.c in the code snippets that can be downloaded from the TI Wiki:

#include <msp430.h>

int main(void)
{
  WDTCTL = WDTPW + WDTHOLD;                 // Stop WDT
  P1DIR |= 0x01;                            // P1.0 output
  TACTL = TASSEL_2 + MC_2 + TAIE;           // SMCLK, contmode, interrupt

  _BIS_SR(LPM0_bits + GIE);                 // Enter LPM0 w/ interrupt
}

// Timer_A3 Interrupt Vector (TAIV) handler
#pragma vector=TIMERA1_VECTOR
__interrupt void Timer_A(void)
{
 switch( TAIV )
 {
   case  2: break;                          // CCR1 not used
   case  4: break;                          // CCR2 not used
   case 10: P1OUT ^= 0x01;                  // overflow
            break;
 }
}

The key is checking the TAIV register to see what caused the interrupt. Take a look at page 416 of the CC430 Family User's Guide:

Now the code example is looking for a value of 10 in the TAIV register and the User Guide indicates that 0x0E is the overflow. So, again, check your specific chip's documentation. But the TAIV register is what will tell you what the cause of the interrupt is.