HAL_Delay works and doesn't work

I'm still very new to STM32 processors, and using CubeMX to generate my basic code structure (for TrueStudio). In the code below, if I uncomment code section A, the yellow LED blinks, but not evenly...

• At low values such HAL_Delay(100), the high time is always 100 or 101ms, but the low time is sometimes 100ms and sometimes 87ms.
• At higher values, such as HAL_Delay(500), the high time is consistently 390ms and low time is less than 1ms.
• Using HAL_Delay(1000) instead gives me the same results as HAL_Delay(500);

What am I missing here?

Now, if I comment out section A, so that section B runs, the red LED comes on, but then the code hangs at the HAL_Delay(1000) so the yellow LED never comes on. If I drop that to HAL_Delay(100), the red LED comes on again, but the yellow LED blinks at approx 2.5Hz. There are no other timers or interrupts running.

I don't know what to check next. If this is somehow expected behaviour, which doc explains how this is supposed to work?

Thanks

/* USER CODE BEGIN 2 */
 
// HAL_TIM_Base_Start_IT(&htim17);
 
 // Code section A...
 while (1)
 {
	 HAL_GPIO_TogglePin(IENC1_GPIO_Port, IENC1_Pin);		// Toggle yellow LED
	 HAL_Delay(500);
 }
 
 // Code section B...
 HAL_GPIO_WritePin(IENC0_GPIO_Port, IENC0_Pin, GPIO_PIN_SET);		// Red LED on
 HAL_Delay(1000);
 HAL_GPIO_WritePin(IENC1_GPIO_Port, IENC1_Pin, GPIO_PIN_SET);		// Yellow LED on
 while(1);
 
 ...