TM4C123G Launchpad Configuring multiple ADC sequencer

Afternoon all, 

I am having difficulties configuring the ADCs on the launchpad. Here is my code:

// select reference positive
    #ifndef LAUNCHPAD
    ADCReferenceSet(ADC0_BASE,  ADC_REF_EXT_3V);
    ADCReferenceSet(ADC1_BASE,  ADC_REF_EXT_3V);
    #endif
    
    #ifdef LAUNCHPAD
    //Enable Pin inputs
    SysCtlPeripheralEnable(SYSCTL_PERIPH_ADC0);
    SysCtlPeripheralEnable(SYSCTL_PERIPH_GPIOE);
    GPIOPinTypeADC( GPIO_PORTE_BASE, GPIO_PIN_3 );
    GPIOPinTypeADC( GPIO_PORTE_BASE, GPIO_PIN_2 );

    // Enable the first sample sequencer to capture the value of channel 0 when
    // the processor trigger occurs.
    ADCSequenceConfigure(ADC0_BASE, SEQ1, ADC_TRIGGER_ALWAYS, PRIORITY0);
    ADCSequenceStepConfigure( ADC0_BASE, SEQ1, STEP0, ADC_CTL_IE | ADC_CTL_END | ADC_CTL_CH0);
    ADCSequenceStepConfigure( ADC0_BASE, SEQ1, STEP1, ADC_CTL_IE | ADC_CTL_END | ADC_CTL_CH1);

    #endif
    //setup interrupts
    ADCIntRegister(ADC0_BASE, SEQ1, ADCinterruptSequencer1);
    ADCIntEnable(ADC0_BASE, SEQ1);
    ADCIntClear(ADC0_BASE, SEQ1);

The issue I am seeing is the ADC on ADC0 is being mirrored in the value from ADC1 (and so on with more added in the chain). I can see voltage changes on the ADC0 input pin being reflected in the value displayed on the screen. However this is also reflected in the value I read back from ADC1. 

I am only using 0 and 3V3 from the board so I have no electronic issues. I am simply trying to reflect a voltage above 500 counts as a LED on using the onboard RGB LED. One colour for each channel. I can see intermediate values (ie floating values) through the UART interface. Otherwise the code performs as expected.

I suspect the issue lays in the configuration somewhere. Anyone any ideas? Thanks :)