Sequence on embedded C code skipping certain flags

Question

I am developing some code for the MSP-EXP430FR5994, specifically code using the MSP430's ADC. My plan for the ADC is to run a dual-channel ADC capture. However, I have only been able to run the code within the first channel.

Here is my relevant ADC code.

#include <msp430.h>
#include <stdio.h>

int main(void)
{
    WDTCTL = WDTPW | WDTHOLD;               // Stop WDT

    // GPIO Setup
    P1OUT &= ~BIT0;                         // Clear LED to start
    P1DIR |= BIT0 | BIT1 | BIT2 ;
    P1SEL1 |= BIT3 | BIT4 ;
    P1SEL0 |= BIT3 | BIT4 ;                 // 1.2 set to TA1.1, 1.3 and 1.4 set to ADC input (A3, A4)
    P1SEL0 |= BIT2 ;                        // Check p88-90_s for what the hell we're doing in the last 3 lines

    // Disable the GPIO power-on default high-impedance mode to activate
    // previously configured port settings
    PM5CTL0 &= ~LOCKLPM5;
    P1OUT |= BIT0;

    // Clock System Setup
    CSCTL0_H = CSKEY_H;                     // Unlock CS registers
    CSCTL1 = DCOFSEL_3;                     // Set DCO to 4MHz (p105)
    CSCTL2 = SELA__VLOCLK | SELS__DCOCLK | SELM__DCOCLK;   // Set clock source
    CSCTL3 = DIVA__1 | DIVS__4 | DIVM__1;   // Set all dividers, clock speed 1MHz
    CSCTL0_H = 0;

    ADC12CTL0 = ADC12SHT0_0 | ADC12MSC | ADC12ON;      // Sampling time, S&H=4, ADC12 on [p893, CTL0 = control 0, SHT0_0 = sample & hold time, knowledge of register value from p88_s]

    ADC12CTL1 = ADC12SHP | ADC12SHS_4 | ADC12CONSEQ_3; // Use TA1.1 to trigger, (SHP means using sample timer (p897), SHS means "sample-and-hold source select" (p895, p84_s)
                                                       // which selects which source is used to activate sampling (4 being TA1.1 because of p84_s), CONSEQ_3 = Conversion sequence select,
                                                       // 3 means repeated-multiple-channel which means multiple channels are converted and sampled, memory gets overriden everytime (p881)
    ADC12CTL2 |= ADC12RES_2;                // 12-bit conversion results, p897
    ADC12CTL3 |= ADC12CSTARTADD_3;          // Use MEM3/MCTL3 as first, p898

    ADC12MCTL3 = ADC12INCH_3;               // A3 ADC input select from Input Channel 3 (p901), output to MEM3
    ADC12MCTL4 = ADC12INCH_4 | ADC12EOS;    // A4 ADC input select, also setting End of sequence bit at A4

    ADC12IER0 |= ADC12IE3 | ADC12IE4 ;      // Enable ADC interrupt [IER = interrupt enable, for IFG0 bit, which tells us when the sequence is complete]
    ADC12CTL0 |= ADC12ENC | ADC12SC;        // Start sampling/conversion

    // Configure TimerA1.1 to periodically trigger the ADC12
    TA1CCR0 = 31250-1;                      // PWM Period for TA1, change to 32Hz, 31250/1000000 = /32
    TA1CCTL1 = OUTMOD_3;                    // TACCR1 set/reset (Shape of set/reset in p652)

    TA1CCR1 = 15625;                          // TACCR1 PWM Duty Cycle
    TA1CTL = TASSEL__SMCLK | MC__UP;        // SMCLK, up mode
    
    __bis_SR_register(LPM0_bits | GIE);     // Enter LPM0, enable interrupts

}

// ADC12 interrupt service routine
#if defined(__TI_COMPILER_VERSION__) || defined(__IAR_SYSTEMS_ICC__)
#pragma vector=ADC12_B_VECTOR
__interrupt void ADC12ISR (void)
#elif defined(__GNUC__)
void __attribute__ ((interrupt(ADC12_B_VECTOR))) ADC12ISR (void)
#else
#error Compiler not supported!
#endif
{
    switch(__even_in_range(ADC12IV, ADC12IV__ADC12RDYIFG))
    {
                                            //Some other flags that were not in use have been removed from this sample. Please let me know if these flags are needed to replicate my code.
        case ADC12IV__ADC12IFG3:            // Vector 18:  ADC12MEM3
            //P1OUT ^= BIT5;
            printf("Got here 3.\n");
            break;
        case ADC12IV__ADC12IFG4:           // Vector 20:  ADC12MEM4
            //P1OUT ^= BIT5;
            printf("Got here 4.\n");
            ADC12MCTL4 |= ADC12EOS;
            break;
        default: break;
    }
}

Please let me know if there's any obvious C syntax I have misplaced. I am aware this is embedded systems (while this is Stackoverflow) but I'm reluctant to dismiss any possibilities. Also, please let me know if any more information is needed.