Electronic – Entering stop mode on STM32L011 only works first time

I have a very typical application here – long periods of minimal current consumption (15 minutes to 24 hours sleep duration) with short periods of activity in between. In my particular case, this is mostly ADC and GPIO manipulation (which explains some of the extra initialisation in my code which is unused) but for this example, I am just trying to achieve the following:

1. Turn LED on
2. Delay 1000ms (using HAL delay – don't care about efficiency here)
3. Turn LED off
4. Enter Stop mode
5. Have RTC Wakeup Timer return me to Step 1. after 5 seconds

So far this works well for the first loop through – I see the LED turn on, turn off after 1000ms, stay off for 5 seconds (current draw drops to approx. 2uA) and then turn on again. However, the LED never turns off again. I can't use SWD to debug this as the board seems to never enter Stop mode with SWD debugging active.

My code (partially generated by STM32CubeMX and partially from reading docs) is as below:

#include "main.h"
#include "stm32l0xx_hal.h" // specific target MCU is STM32L011D3P6

ADC_HandleTypeDef hadc;

RTC_HandleTypeDef hrtc;

void SystemClock_Config(void);
void Error_Handler(void);
static void MX_GPIO_Init(void);
static void MX_ADC_Init(void);
static void MX_RTC_Init(void);

void SystemPower_Config(void);

int main(void)
{
  HAL_Init();

  SystemClock_Config();

  MX_GPIO_Init();
  MX_ADC_Init();
  MX_RTC_Init();

  SystemPower_Config();

  #ifdef DEBUG
    HAL_DBGMCU_EnableDBGStopMode();
  #else
    HAL_DBGMCU_DisableDBGStopMode();
  #endif

  while (1)
  {
    HAL_GPIO_WritePin(LED_1_GPIO_Port, LED_1_Pin, GPIO_PIN_SET);
    HAL_Delay(1000);
    HAL_GPIO_WritePin(LED_1_GPIO_Port, LED_1_Pin, GPIO_PIN_RESET);

    HAL_RTCEx_DeactivateWakeUpTimer(&hrtc);

    if (HAL_RTCEx_SetWakeUpTimer_IT(&hrtc, 5, RTC_WAKEUPCLOCK_CK_SPRE_16BITS) != HAL_OK)
    {
      Error_Handler();
    }

    __HAL_RCC_PWR_CLK_ENABLE();
    HAL_PWR_EnterSTOPMode(PWR_LOWPOWERREGULATOR_ON, PWR_STOPENTRY_WFI);

  }  
}

void SystemClock_Config(void)
{
  RCC_OscInitTypeDef RCC_OscInitStruct;
  RCC_ClkInitTypeDef RCC_ClkInitStruct;
  RCC_PeriphCLKInitTypeDef PeriphClkInit;

  __HAL_PWR_VOLTAGESCALING_CONFIG(PWR_REGULATOR_VOLTAGE_SCALE1);

  RCC_OscInitStruct.OscillatorType = RCC_OSCILLATORTYPE_HSI|RCC_OSCILLATORTYPE_LSI
                              |RCC_OSCILLATORTYPE_MSI;
  RCC_OscInitStruct.HSIState = RCC_HSI_DIV4;
  RCC_OscInitStruct.HSICalibrationValue = 16;
  RCC_OscInitStruct.LSIState = RCC_LSI_ON;
  RCC_OscInitStruct.MSIState = RCC_MSI_ON;
  RCC_OscInitStruct.MSICalibrationValue = 0;
  RCC_OscInitStruct.MSIClockRange = RCC_MSIRANGE_4;
  RCC_OscInitStruct.PLL.PLLState = RCC_PLL_NONE;
  if (HAL_RCC_OscConfig(&RCC_OscInitStruct) != HAL_OK)
  {
    Error_Handler();
  }

  RCC_ClkInitStruct.ClockType = RCC_CLOCKTYPE_HCLK|RCC_CLOCKTYPE_SYSCLK
                              |RCC_CLOCKTYPE_PCLK1|RCC_CLOCKTYPE_PCLK2;
  RCC_ClkInitStruct.SYSCLKSource = RCC_SYSCLKSOURCE_MSI;
  RCC_ClkInitStruct.AHBCLKDivider = RCC_SYSCLK_DIV1;
  RCC_ClkInitStruct.APB1CLKDivider = RCC_HCLK_DIV1;
  RCC_ClkInitStruct.APB2CLKDivider = RCC_HCLK_DIV1;

  if (HAL_RCC_ClockConfig(&RCC_ClkInitStruct, FLASH_LATENCY_0) != HAL_OK)
  {
    Error_Handler();
  }

  PeriphClkInit.PeriphClockSelection = RCC_PERIPHCLK_RTC;
  PeriphClkInit.RTCClockSelection = RCC_RTCCLKSOURCE_LSI;
  if (HAL_RCCEx_PeriphCLKConfig(&PeriphClkInit) != HAL_OK)
  {
    Error_Handler();
  }

  HAL_SYSTICK_Config(HAL_RCC_GetHCLKFreq()/1000);

  HAL_SYSTICK_CLKSourceConfig(SYSTICK_CLKSOURCE_HCLK);

  HAL_NVIC_SetPriority(SysTick_IRQn, 0, 0);
}

static void MX_ADC_Init(void)
{

  ADC_ChannelConfTypeDef sConfig;

  hadc.Instance = ADC1;
  hadc.Init.OversamplingMode = DISABLE;
  hadc.Init.ClockPrescaler = ADC_CLOCK_ASYNC_DIV16;
  hadc.Init.Resolution = ADC_RESOLUTION_12B;
  hadc.Init.SamplingTime = ADC_SAMPLETIME_160CYCLES_5;
  hadc.Init.ScanConvMode = ADC_SCAN_DIRECTION_FORWARD;
  hadc.Init.DataAlign = ADC_DATAALIGN_RIGHT;
  hadc.Init.ContinuousConvMode = DISABLE;
  hadc.Init.DiscontinuousConvMode = DISABLE;
  hadc.Init.ExternalTrigConvEdge = ADC_EXTERNALTRIGCONVEDGE_NONE;
  hadc.Init.ExternalTrigConv = ADC_SOFTWARE_START;
  hadc.Init.DMAContinuousRequests = DISABLE;
  hadc.Init.EOCSelection = ADC_EOC_SEQ_CONV;
  hadc.Init.Overrun = ADC_OVR_DATA_PRESERVED;
  hadc.Init.LowPowerAutoWait = DISABLE;
  hadc.Init.LowPowerFrequencyMode = ENABLE;
  hadc.Init.LowPowerAutoPowerOff = ENABLE;
  if (HAL_ADC_Init(&hadc) != HAL_OK)
  {
    Error_Handler();
  }

  sConfig.Channel = ADC_CHANNEL_1;
  sConfig.Rank = ADC_RANK_CHANNEL_NUMBER;
  if (HAL_ADC_ConfigChannel(&hadc, &sConfig) != HAL_OK)
  {
    Error_Handler();
  }

  sConfig.Channel = ADC_CHANNEL_4;
  if (HAL_ADC_ConfigChannel(&hadc, &sConfig) != HAL_OK)
  {
    Error_Handler();
  }

  sConfig.Channel = ADC_CHANNEL_TEMPSENSOR;
  if (HAL_ADC_ConfigChannel(&hadc, &sConfig) != HAL_OK)
  {
    Error_Handler();
  }

}

static void MX_RTC_Init(void)
{

  RTC_TimeTypeDef sTime;
  RTC_DateTypeDef sDate;

  hrtc.Instance = RTC;
  hrtc.Init.HourFormat = RTC_HOURFORMAT_24;
  hrtc.Init.AsynchPrediv = 127;
  hrtc.Init.SynchPrediv = 255;
  hrtc.Init.OutPut = RTC_OUTPUT_DISABLE;
  hrtc.Init.OutPutRemap = RTC_OUTPUT_REMAP_NONE;
  hrtc.Init.OutPutPolarity = RTC_OUTPUT_POLARITY_HIGH;
  hrtc.Init.OutPutType = RTC_OUTPUT_TYPE_OPENDRAIN;
  if (HAL_RTC_Init(&hrtc) != HAL_OK)
  {
    Error_Handler();
  }

  sTime.Hours = 0x0;
  sTime.Minutes = 0x0;
  sTime.Seconds = 0x0;
  sTime.DayLightSaving = RTC_DAYLIGHTSAVING_NONE;
  sTime.StoreOperation = RTC_STOREOPERATION_RESET;
  if (HAL_RTC_SetTime(&hrtc, &sTime, RTC_FORMAT_BCD) != HAL_OK)
  {
    Error_Handler();
  }

  sDate.WeekDay = RTC_WEEKDAY_MONDAY;
  sDate.Month = RTC_MONTH_JANUARY;
  sDate.Date = 0x1;
  sDate.Year = 0x0;

  if (HAL_RTC_SetDate(&hrtc, &sDate, RTC_FORMAT_BCD) != HAL_OK)
  {
    Error_Handler();
  }
}

static void MX_GPIO_Init(void)
{

  GPIO_InitTypeDef GPIO_InitStruct;

  __HAL_RCC_GPIOC_CLK_ENABLE();
  __HAL_RCC_GPIOA_CLK_ENABLE();

  HAL_GPIO_WritePin(SENSOR_EN_GPIO_Port, SENSOR_EN_Pin, GPIO_PIN_RESET);

  HAL_GPIO_WritePin(GPIOA, LED_2_Pin|LED_1_Pin|LED_0_Pin, GPIO_PIN_RESET);

  GPIO_InitStruct.Pin = SELF_TEST_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_INPUT;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  HAL_GPIO_Init(SELF_TEST_GPIO_Port, &GPIO_InitStruct);

  GPIO_InitStruct.Pin = SENSOR_EN_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(SENSOR_EN_GPIO_Port, &GPIO_InitStruct);

  GPIO_InitStruct.Pin = LED_2_Pin|LED_1_Pin|LED_0_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(GPIOA, &GPIO_InitStruct);

}


void HAL_RTCEx_WakeUpTimerEventCallback(RTC_HandleTypeDef *hrtc){
  __HAL_PWR_CLEAR_FLAG(PWR_FLAG_WU);
}

void SystemPower_Config(void)
{
  __HAL_RCC_PWR_CLK_ENABLE();
  HAL_PWREx_EnableUltraLowPower();
}

void Error_Handler(void)
{
  while(1) 
  {
  } 
}

Main.h simply maps GPIO pins to the names used in the code – happy to post that if it's useful. Can anyone point out where I am going wrong here? Or suggest a helpful debug approach? (given that I sadly can't do much register poking with SWD ruining my ability to go into sleep mode)