STM32 HAL_GPIO_WritePin not working

Question

I am using an NUCLEO-F411RE and try to use the GPIO with HAL. Its the first time i am facing this problem. I initialized the GPIO Pins like this:

static void MX_GPIO_Init(void)
{
      GPIO_InitTypeDef GPIO_InitStruct = {0};

      /* GPIO Ports Clock Enable */
      __HAL_RCC_GPIOC_CLK_ENABLE();
      __HAL_RCC_GPIOH_CLK_ENABLE();
      __HAL_RCC_GPIOA_CLK_ENABLE();
      __HAL_RCC_GPIOB_CLK_ENABLE();

      /*Configure GPIO pin Output Level */
      HAL_GPIO_WritePin(User_LED_GPIO_Port, User_LED_Pin, GPIO_PIN_RESET);

      /*Configure GPIO pin Output Level */
      HAL_GPIO_WritePin(GPIOA, O_Reset_Pin|O_Wake_Up_Pin, GPIO_PIN_RESET);

      /*Configure GPIO pin Output Level */
      HAL_GPIO_WritePin(GPIOC, O_Boot_Pin|O_Mode_1_Pin, GPIO_PIN_RESET);

      /*Configure GPIO pins : O_Reset_Pin O_Wake_Up_Pin */
      GPIO_InitStruct.Pin = O_Reset_Pin|O_Wake_Up_Pin;
      GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
      GPIO_InitStruct.Pull = GPIO_PULLUP;
      GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
      HAL_GPIO_Init(GPIOA, &GPIO_InitStruct);

      /*Configure GPIO pin : O_Boot_Pin */
      GPIO_InitStruct.Pin = O_Boot_Pin;
      GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
      GPIO_InitStruct.Pull = GPIO_NOPULL;
      GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
      HAL_GPIO_Init(GPIOC, &GPIO_InitStruct);
}

I removed some PIN init code because i am facing the Problem with the Reset and Wake_up Pin which are part of GPIOA. For test behaviour i keep the BOOT Pin from GPIOC.

One side question, after the initialisation as GPIO_PULLUP. Why are these two pins on a low level. Shouldn't they be as default on a high level?

Because of that i Set this Pins to High bevor my while(1) loop like this:

HAL_GPIO_WritePin(O_Boot_GPIO_Port, O_Boot_Pin, GPIO_PIN_SET);
HAL_GPIO_WritePin(O_Reset_GPIO_Port, O_Reset_Pin, GPIO_PIN_SET);
HAL_GPIO_WritePin(O_Wake_Up_GPIO_Port, O_Wake_Up_Pin, GPIO_PIN_SET);

The record of my logic analyzer looks like this:

The Reset & Wake_up pin from GPIOA are dropping back to low level. But the boot Pin keeps high level like expected. I started a debug session and realized, when i call the Hal_delay() function these two pins are dropping back to low level. So i just put a HAL_delay() function between the WritePin function.

HAL_GPIO_WritePin(O_Boot_GPIO_Port, O_Boot_Pin, GPIO_PIN_SET);
HAL_Delay(10);
HAL_GPIO_WritePin(O_Reset_GPIO_Port, O_Reset_Pin, GPIO_PIN_SET);
HAL_Delay(10);
HAL_GPIO_WritePin(O_Wake_Up_GPIO_Port, O_Wake_Up_Pin, GPIO_PIN_SET);
HAL_Delay(10);

The logic analyzer looks like this:

As you can see, the Pin level drop to low after i use the HAL_delay function. But just for the GPIOA Pins.

I actually know what problem i have! In the Timer Callback function i toggle two pins PA8 and PA11. If i remove this code everything works fine. So the Problem is my Bitmanipulation on GPIOA.

Here is the function

void HAL_TIM_PWM_PulseFinishedCallback(TIM_HandleTypeDef *htim)
{
    static uint8_t countClkCycles;

    countClkCycles++;    

    if(countClkCycles >= 40)
    {
        k++;
    }
        if(k == 10)
        {
            k=0;
        }
    else
    {
        if(goldcode1[k] == 1)
        {
                GPIOA->ODR ^= (1<<11);                  // Toggle output GPIO PA11
        }
        else
        {
            GPIOA->BSRR = (1<<27);
        }
    }


    if(countClkCycles >= 40)
    {
        int j=i+1;

        if(j == 10)
        {
            j=0;
        }
        if(goldcode1[i] == goldcode1[j])
        {
                GPIOA->ODR ^= (1<<8);                               //Toggle output GPIOA PA8
        }
        else
        {
                //GPIOA->BSRR = (1<<24);
                if(goldcode1[i] == 1)
                {
                        //GPIOA->ODR = (1<<8);                          //sets output GPIOA PA8
                        GPIOA->BSRR = (1<<24);
                }
                else
                {
                        //GPIOA->BSRR = (1<<24);                        //resets output GPIOA PA8
                        GPIOA->ODR = (1<<8);                            //sets output GPIOA PA8
                }
        }
        i=j;

        //TIM2->CCMR1 ^= 1 << 4;
        countClkCycles = 0;
    }
    else
    {
            GPIOA->ODR ^= (1<<8);                                 //Toggle output GPIOA PA8
    }

}

How should i do the Bitmanipulation that i just toggle PA8 and PA11 and not the whole GPIOA register.