MSP430G2955: Pin Oscillator Capsense Counter not counting

Part Number:MSP430G2955

Hi all. I have an application on the MSP430G2955 that measures capacitance from 6 elements in a row. Unfortunately, only one of the six pads (Pads 0-5, only pad 1 works consistently) makes TA0R count during the WDT gate timer. When using the debugger to check the value of TA0R after waking up from LPM3, TA0R is only non-zero for Pad 1 and occasionally Pad2 (every 5 readings). My pin mappings have been verified and additionally when probing the pads with an oscilloscope I can see the correct signal on each pad (pulse every 500ms where each pulse's top is made up of the RO-frequency-modulated count signal). The oscillator seems to be operating correctly but the timer is not counting.

Here is my capsense code:

void TI_CTS_RO_PINOSC_TA0_WDTp_HAL(const struct Sensor *group, uint16_t *counts)
{
    uint8_t i = 0;

    //** Context Save
    //  Status Register:
    //  WDTp: IE1, WDTCTL
    //  TIMERA0: TA0CTL, TA0CCTL1
    //  Ports: PxSEL, PxSEL2
    uint8_t contextSaveSR;
    uint8_t contextSaveIE1;
    uint16_t contextSaveWDTCTL;
    uint16_t contextSaveTA0CTL, contextSaveTA0CCTL1, contextSaveTA0CCR1;
    uint8_t contextSaveSel, contextSaveSel2;

    contextSaveSR = __get_SR_register();
    contextSaveIE1 = IE1;
    contextSaveWDTCTL = WDTCTL;
    contextSaveWDTCTL &= 0x00FF;
    contextSaveWDTCTL |= WDTPW;
    contextSaveTA0CTL = TA0CTL;
    contextSaveTA0CCTL1 = TA0CCTL1;
    contextSaveTA0CCR1 = TA0CCR1;

    //** Setup Measurement timer***************************************************
    // Choices are TA0,TA1,TB0,TB1,TD0,TD1 these choices are pushed up into the
    // capacitive touch layer.

    // Configure and Start Timer
    TA0CTL = TASSEL_3 + MC_2;                              // INCLK, cont mode // changed from TASSEL_3
    TA0CCTL1 = CM_3 + CCIS_2 + CAP;                        // Pos&Neg,GND,Cap
    IE1 |= WDTIE;                                          // enable WDT interrupt
    // Loop across all 6 pads
    for (i = 0; i < (group->numElements); i++)
    {
        // Context Save
    	contextSaveSel = *((group->arrayPtr[i])->inputPxselRegister);
    	contextSaveSel2 = *((group->arrayPtr[i])->inputPxsel2Register);

        // Configure Ports for relaxation oscillator (in English... enable Capacitive sensing)
    	*((group->arrayPtr[i])->inputPxselRegister) &= ~((group->arrayPtr[i])->inputBits);
    	*((group->arrayPtr[i])->inputPxsel2Register) |= ((group->arrayPtr[i])->inputBits);

        //**  Setup Gate Timer ********************************************************
        // Set duration of sensor measurment
        WDTCTL = (WDTPW + WDTTMSEL + (group->measGateSource) + (group->accumulationCycles)); // wdt comes from aclk (gate source), aclk/512 -> use aclk for capsense
        TA0CTL |= TACLR;                                   // Clear Timer_A TAR
        if (group->measGateSource == GATE_WDT_ACLK)
        {
            __bis_SR_register(LPM3_bits + GIE);            // Wait for WDT interrupt
        }
        else
        {
            __bis_SR_register(LPM0_bits + GIE);            // Wait for WDT interrupt
        }
        // every other pad the reference signal is alternated between GND and VCC (this causes rising and falling trigger events)
        // this causes a transition that starts the calculation of capacitance
        TA0CCTL1 ^= CCIS0;    // Create SW capture of CCR1   (setting compare source to VCC)
        counts[i] = TA0CCR1;     // Save result - BREAKPOINT HERE TO CHECK TA0R and TA0CCR1
        WDTCTL = WDTPW + WDTHOLD;                          // Stop watchdog timer
                                                          
        // Context Restore
        *((group->arrayPtr[i])->inputPxselRegister) = contextSaveSel;
        *((group->arrayPtr[i])->inputPxsel2Register) = contextSaveSel2;
    }
    // End Sequence
    // Context Restore
    __bis_SR_register(contextSaveSR);
    if (!(contextSaveSR & GIE))
    {
        __bic_SR_register(GIE);                            //
    }
    IE1 = contextSaveIE1;
    WDTCTL = contextSaveWDTCTL;
    TA0CTL = contextSaveTA0CTL;
    TA0CCTL1 = contextSaveTA0CCTL1;
    TA0CCR1 = contextSaveTA0CCR1;
}

Any help or ideas would be greatly appreciated. Feel free to ask questions; I am happy to provide more info.