Solved
DMA _Init() being called in wrong place by code generator
The code generator is inserting the DMA_Init() and BDMA_Init functions in the wrong place, leaving DMA not working unless I manually move them after every call code generator run.
I place them in the USER CODE segment above the INIT segment then remove the auto generated versions each time otherwise DMA doesn't work.
/* USER CODE BEGIN SysInit */
MX_BDMA_Init();
MX_DMA_Init();
/* USER CODE END SysInit */
/* Initialize all configured peripherals */
MX_GPIO_Init();
MX_USART3_UART_Init();
MX_USART2_UART_Init();
MX_TIM2_Init();
MX_DMA_Init(); // PLACED HERE BY CODE GENERATOR
MX_LPUART1_UART_Init();
MX_BDMA_Init(); // PLACED HERE BY CODE GENERATOR
MX_I2C1_Init();
MX_TIM3_Init();
/* USER CODE BEGIN 2 */