MSP430FR5994: Reading multiple ADC channels

Part Number: MSP430FR5994

Tool/software:

I am trying to read from A3 and A4 inputs to the processor. I can read A3 fine, but when I try and read A4, I get the same value. With the debugger I can see that I am correctly changing ADC12MCTL0 depending on which parameter I call the function with, so I am assuming there is something else wrong with how I am reading the result registers? Any help would be greatly appreciated.

uint16_t adcResult = 0x0000;

void initADC(){
    while(REFCTL0 & REFGENBUSY);            // If ref generator busy, WAIT
    REFCTL0 |= REFVSEL_2 | REFON;           // Select internal ref = 2.5V

    ADC12CTL0 = ADC12SHT0_2 | ADC12ON;
    ADC12CTL1 = ADC12SHP;                   // ADCCLK = MODOSC; sampling timer
    ADC12CTL2 |= ADC12RES_2;                // 12-bit conversion results
}

uint16_t sampleADC(ADC_Input channel){
    //select right channels from the ADC
    switch(channel){
        case ADC_CH_REG_3V3:
            ADC12MCTL0 = ADC12INCH_4 | ADC12VRSEL_1;       // A1 ADC input select; Vref=+VRef
            break;
        case ADC_CH_INA241:
            ADC12MCTL0 = ADC12INCH_3 | ADC12VRSEL_1;
            break;
    }

    while(!(REFCTL0 & REFGENRDY)); //make sure reference has settled
    ADC12IER0 |= ADC12IE0;              // Enable ADC conv complete interrupt
    ADC12CTL0 |= ADC12ENC | ADC12SC;    // Enable and start sampling/conversion    

    __bis_SR_register(LPM0_bits + GIE);      // Enter LPM0 w/ interrupts

    return adcResult;
}

//**********************************************************************************************
//** ADC Interrupt routine *********************************************************************
//** Called when the corresponding ADC12MEMx memory register is loaded with a conversion result
//**********************************************************************************************
#pragma vector = ADC12_B_VECTOR
__interrupt void ADC12_ISR(void)
{
    switch(__even_in_range(ADC12IV, ADC12IV__ADC12RDYIFG))
    {
        case ADC12IV__ADC12IFG0:            // Vector 12:  ADC12MEM0 Interrupt
            adcResult = ADC12MEM0; 
            // Exit from LPM0 and continue executing main
            __bic_SR_register_on_exit(LPM0_bits);
            break;
    }
}