CCS/MSP430FR2311: FR2000 Multiple Timebases Example porting to 2311

Thanks for the help, Bruce! That was indeed the issue! And sure enough, I was fiddling with the RTC before trying this code, and I didn't power-cycle in between. 

A quick follow-up question though -- Why does it take about 5 seconds for the LEDs to show the first color every time? 

I've now initialized the RTC and added a function to count seconds and increment the "selected" value every 1 second. I see the LED come on only after 5 or so seconds of running the program every time.

#include<msp430.h>
#include<stdint.h>

//  Contains the low (on) period for the RGB LEDs for each color selection
const uint8_t colorsLow[12][3] = {
                           //{R, G, B}
                           {134,1,1},   //RED
                           {134,15,1},  //RED-ORANGE
                           {134,20,1},  //ORANGE
                           {134,30,1},  //ORANGE-YELLOW
                           {134,55,1},  //YELLOW
                           {67,80,1},   //YELLOW-GREEN
                           {1,134,1},   //GREEN
                           {1,134,134}, //GREEN-BLUE
                           {1,1,134},   //BLUE
                           {67,1,134},  //BLUE-PURPLE
                           {134,1,134}, //PURPLE
                           {134,1,80}   //PURPLE-RED
};
//  Contains the high (off) period for the RGB LEDs for each color selection
const uint8_t colorsHigh[12][3] = {
                           //{R, G, B}
                           {1,134,134}, //RED
                           {1,120,134}, //RED-ORANGE
                           {1,115,134}, //ORANGE
                           {1,100,134}, //ORANGE-YELLOW
                           {1,80,134},  //YELLOW
                           {68,55,134}, //YELLOW-GREEN
                           {134,1,134}, //GREEN
                           {134,1,1},   //GREEN-BLUE
                           {134,134,1}, //BLUE
                           {68,134,1},  //BLUE-PURPLE
                           {1,134,1},   //PURPLE
                           {1,134,55}   //PURPLE-RED
};

uint8_t selected;   //Used to track the current color selection

/**
 * main.c
 */
void main(void)
{
    WDTCTL = WDTPW | WDTHOLD;               // Stop watchdog timer

    selected = 0;                           // Default to Red
    RTCCTL=0;

    // Configure UART
    // From user's Guide Table of Baud Rates, 9600 baud at BRCLK = 32768
    // UCOS16 = 0
    // UCBRx = 3
    // UCBRFx = 0
    // UCBRSx = 0x92
    UCA0CTLW0 = UCSWRST | UCSSEL__ACLK;
    UCA0BRW = 3;
    UCA0MCTLW = 0x9200;
    UCA0CTLW0 &= ~UCSWRST;              // Initialize eUSCI
    UCA0IE = UCRXIE;                    // Enable USCI_A0 RX interrupt

    // Configure GPIO
//    PASEL0 = BIT6 | BIT7 | BIT8 | BIT9; // TB0.1 and 0.2, UCA0 RXD and TXD
//    PADIR = BIT8 | BIT9 | BIT0;         // TB0.1, 0.2, 0.0 (on P1.0)
//    PAOUT = 0;

    P1SEL0 = BIT6 + BIT7; // Enable UART function on p1.6 & 1.7

    P1DIR = BIT0;           // Set P1.0 to output
    P2SEL0 = BIT0 + BIT1;   // Enable secondary function of TB1 output on given pins
    P2DIR =  BIT0 + BIT1;   // Enable output on p2.0 & 2.1
    PAOUT = 0;  // shut everything

    PM5CTL0 &= ~LOCKLPM5;               // Disable the GPIO power-on default
                                        // high-impedance mode to activate
                                        // previously configured port settings
    // RTC count re-load compare value at 32.
    // 1024/32768 * 32 = 1 sec.
    RTCMOD = 32-1;
//    RTCMOD = 4 - 1;
    // Initialize RTC
    // Source = ACLK = REFO, divided by 1024
    SYSCFG2 |= RTCCKSEL;                    // Select ACLK as RTC clock
    RTCCTL = RTCSS_1 | RTCSR | RTCPS__1024 | RTCIE;

    // Set up Timer B in continuous mode for multiple time base PWMs.
    // See app note SLAA513 for theory.
    TB1CCTL0 = CCIS_0 + OUTMOD_4 + CCIE;    // CCR0 toggle, interrupt enabled
    TB1CCTL1 = CCIS_0 + OUTMOD_4 + CCIE;    // CCR1 toggle, interrupt enabled
    TB1CCTL2 = CCIS_0 + OUTMOD_4 + CCIE;    // CCR2 toggle, interrupt enabled

    // REF0CLK/4 = 8192 is used for TBCLK so that the period of 60Hz can be
    // generated with TB0CCRx values totaling only 135 for the period of 60Hz
    // PWM. This is less than 255, so that the lookup table can be made of 8-bit
    // values, saving additional FRAM space on small devices.
    TB1CTL = TBSSEL__ACLK + ID__4 + MC_2 + TBCLR;   // ACLK, contmode, clear TAR


    __bis_SR_register(LPM3_bits | GIE);     // Go to LPM3 with interrupts
    __no_operation();
}

void incrementSeconds(){

    if(selected > 11)       // If value out of range, set default 0 (red)
        {
            selected = 0;
        }
    else selected++;
}

// UART interrupt service routine
#pragma vector=USCI_A0_VECTOR
__interrupt void USCI_A0_ISR(void)
{
    selected = UCA0RXBUF;   // Get new value for selected color

    if(selected > 11)       // If value out of range, set default 0 (red)
    {
        selected = 0;
    }
}

// RTC interrupt service routine
#pragma vector=RTC_VECTOR
__interrupt void RTC_ISR(void)
{
    switch (__even_in_range(RTCIV, RTCIV_RTCIF))
    {
    case RTCIV_NONE:
        break;          // No interrupt
    case RTCIV_RTCIF:                  // RTC Overflow
        incrementSeconds();
        break;
    default:
        break;
    }
}

// Timer_B0 interrupt service routine
#pragma vector=TIMER1_B0_VECTOR
__interrupt void TIMER1_B0_ISR (void)
{
    if(P1OUT & BIT0)                        // Check current output level
    {
        TB1CCR0 += colorsLow[selected][2];  // Low period (Blue LED on)
        P1OUT = 0;      // TB0.0 not brought out on pin, so set manually
    }
    else
    {
        TB1CCR0 += colorsHigh[selected][2]; // High period (Blue LED off)
        P1OUT = BIT0;   // TB0.0 not brought out on pin, so set manually
    }
}

// Timer_B1 Interrupt Vector (TBIV) handler
#pragma vector=TIMER1_B1_VECTOR
__interrupt void TIMER1_B1_ISR(void)
{
    switch(__even_in_range(TB1IV,14))
    {
        case 0: break;
        case 2: if(TB1CCTL1 & CCI)          // Check current timer pin state
                {
                    TB1CCR1 += colorsHigh[selected][0]; // High period (Red off)
                }
                else
                {
                    TB1CCR1 += colorsLow[selected][0];  // Low period (Red on)
                }
                break;
        case 4: if(TB1CCTL2 & CCI)          // Check current timer pin state
                {
                   TB1CCR2 += colorsHigh[selected][1];  // High (Green off)
                }
                else
                {
                   TB1CCR2 += colorsLow[selected][1];   // Low period (Green on)
                }
                break;
        default:    break;
    }
}

That did solve the issue of late start! Thanks a ton, Bruce!

I'm just getting started, and hope I don't run into further issues :)