Atmel AVR ADC Inconsistent Sampling Time

I’m running an ATMega1284 at 20MHz. I’ve set the ADC up in free running mode as such:

void SetupADCInFreeRunningMode(uint16_t ref, uint16_t channel, uint16_t leftAdjust, uint16_t clockDiv)
{
    ADMUX |= ref | leftAdjust | channel;
    DIDR0 |= true << ADC3D;
    ADCSRA |= true << ADEN | true << ADATE | true << ADIE | clockDiv;
}

And I’m sampling the ADC into a buffer in the ADC interrupt:

ISR(ADC_vect)
{
    DISABLE_INT;
    ToggleLed(Red);
    if (BufferPosition < ADC_BUFFER_SIZE)
    {
        ADCBuffer[BufferPosition++] = ADCH - (int8_t)127;
    }
    else
    {
        BufferFull = true;
    }
    ENABLE_INT;
}

Since I’m having issues with my Goertzel implementation returning bad results I wanted to check my sample rate. Based on the simulator, this ought to be around 12019Hz.

However, after plugging my data analyzer into the LED pin being toggled, I find that it’s sampling at an inconsistent speed, I get two samples at 12.4kHz followed by one sample at 9.9kHz. Given I disable the other interrupts whilst the sample is being taken, what could be causing this?

---

In order to help debug this I removed everything except the LED toggle:

ISR(ADC_vect)
{
    DISABLE_INT;
    ToggleLed(Red);
    ENABLE_INT;
}

Now I get a consistent (all in us) 80 on, 80 off, 80 on, 80 off, 80 on, 100 off. Does the ADC have to reset every 6 interrupts or something?

---

TIMER1_COMPA was set to run at 200Hz. With this ISR:

ISR(TIMER1_COMPA_vect,  ISR_NOBLOCK)
{
    PushFrame();
}

However, disabling this interrupt so the ADC interrupt is the only one on the system does not help.

---

With an absolutely minimal working example:

//Standard lib includes
#include <stdbool.h>

//AVR includes
#include <avr/io.h>
#include <avr/interrupt.h>
#include <avr/sleep.h>

//Project includes
#include "leds.h"
#include "ADC.h"

//Named Literals
#define COMP_200Hz 12500 //NOTE: Needs 8x prescaler
#define F_CPU 20e6

//Macros
#define ENABLE_INT sei()
#define DISABLE_INT cli()

//Functions
int main(void)
{
    SetupADCInFreeRunningMode(AVCC, ADC3, LAEnabled, CDOneTwoEigth);
    ENABLE_INT;
    StartADC();
    /* Replace with your application code */
    while (true)
    {
        ;
    }
}

ISR(ADC_vect)
{
    ToggleLed(Red);
}

For completeness:

void ToggleLed(Led colour)
{
    switch (colour)
    {
        case Red:
            PORTD ^= true << RED_LED;
            break;
        case Yellow:
            PORTD ^= true << YELLOW_LED;
            break;
        case Green:
            PORTD ^= true << GREEN_LED;
            break;
    }
}

The problem is still occurring.

I’m really stumped on this one.

---

I’ve upped the sample rate on my logic analyser to 8MHz and now get this output.

So something strange is happening periodically.