Modbus communication via STM32F4

Hi

I am using UART5 interrupt handler to receive bytes in Mod-bus protocol.
MCU is STM32f407VGT6. My problem is that UART ISR does not get first 4 bytes from slave.
I have checked signals with scope so I am sure hardware is okay.
my code is in below after a time out I read the buffer but instead of 9 bytes there is only last 5 bytes from slave.

void uart5_configuration(void)
{
        USART_InitTypeDef USART_InitStructure;
  GPIO_InitTypeDef GPIO_InitStructure;

  RCC_AHB1PeriphClockCmd(RCC_AHB1Periph_GPIOC, ENABLE);
  RCC_AHB1PeriphClockCmd(RCC_AHB1Periph_GPIOD, ENABLE);
  RCC_APB1PeriphClockCmd(RCC_APB1Periph_UART5,ENABLE);

  GPIO_PinAFConfig(GPIOC, GPIO_PinSource12, GPIO_AF_UART5);
  GPIO_PinAFConfig(GPIOD, GPIO_PinSource2, GPIO_AF_UART5);

  /* Configure USART2 pins:  Rx and Tx ----------------------------*/
  GPIO_InitStructure.GPIO_Pin =  GPIO_Pin_12;
  GPIO_InitStructure.GPIO_Speed = GPIO_Speed_25MHz;
  GPIO_InitStructure.GPIO_Mode = GPIO_Mode_AF;
  GPIO_InitStructure.GPIO_OType = GPIO_OType_PP;
  GPIO_InitStructure.GPIO_PuPd = GPIO_PuPd_UP;
  GPIO_Init(GPIOC, &GPIO_InitStructure);

  GPIO_InitStructure.GPIO_Pin =  GPIO_Pin_2;
  GPIO_InitStructure.GPIO_Speed = GPIO_Speed_25MHz;
  GPIO_InitStructure.GPIO_Mode = GPIO_Mode_AF;
  GPIO_InitStructure.GPIO_OType = GPIO_OType_PP;
  GPIO_InitStructure.GPIO_PuPd = GPIO_PuPd_UP;
  GPIO_Init(GPIOD, &GPIO_InitStructure);

  USART_InitStructure.USART_BaudRate = 9600;
  USART_InitStructure.USART_WordLength = USART_WordLength_8b;
  USART_InitStructure.USART_StopBits = USART_StopBits_1;
  USART_InitStructure.USART_Parity = USART_Parity_No;
  USART_InitStructure.USART_HardwareFlowControl = USART_HardwareFlowControl_None;
  USART_InitStructure.USART_Mode = USART_Mode_Rx | USART_Mode_Tx;
  USART_Init(UART5, &USART_InitStructure);

  USART_Cmd(UART5,ENABLE);
    /* Enable RXNE interrupt */
  USART_ITConfig(UART5, USART_IT_RXNE, ENABLE);
   /* Enable USART5 global interrupt */
  NVIC_EnableIRQ(UART5_IRQn);
}

void UART5_IRQHandler(void)
{




    /* RXNE handler */
    if(USART_GetITStatus(UART5, USART_IT_RXNE) != RESET)
    {
                        char data;
                        data=USART_ReceiveData(UART5);
                        SYS.RS485_buffer[SYS.USART5_RX_counter]=data;
                        SYS.flag_RS485_RX=1;
                        SYS.flag_USART5_Timeout=0;
                        SYS.USART5_RX_counter++;
                        SYS.flag_RX5=1;
    }
}

void event_RS485(void)
{
        int i;char str[100];

                if(SYS.flag_USART5_Timeout==1) //if time out
                {

                        SYS.RS485_buffer_size=SYS.USART5_RX_counter;
                        print_str(USART1,"rs485");
                        sprintf(str,"<<BYTES:%u>>\r\n",SYS.RS485_buffer_size);
                        uart_out_str(str);
                        for(i=0;i<sizeof(SYS.RS485_buffer);i++)
                        {
                        sprintf(str,"0x%x_",SYS.RS485_buffer[i]);
                        uart_out_str(str);
                        }

                        SYS.flag_RS485_RX=0;     //do not execute this part more
                        SYS.flag_USART5_Timeout=0;

                        SYS.USART5_RX_counter=0; //after time out reset RX buffer counter

                }
}