Problem receiving data through USART using ATmega1284p

//MatlabToMicroTest04
//this code is to test sending data FROM matlab to 1284p, and storing in Flash memory, using uart.c by Joerg wunsch

#include <avr/io.h>
#include <util/delay.h>
#include <avr/inttypes.h>
#include <avr/uart.c>
#include <avr/uart.h>

// Yellow and Green LEDS
#define LED_D5 (1<<5) // yellow
#define LED_D4 (1<<4) // green

//create prototypes for Main
void initialize(void);

FILE uart_str = FDEV_SETUP_STREAM(uart_putchar, uart_getchar, _FDEV_SETUP_RW);

void initialize(void){
	uart_init();
	stdout = stdin = stderr = &uart_str;
	
	}

//*************[START]******code needed for SPI, storing in Flash memory**********************

#define SETBIT(REG,BITNUM)   ((void) (REG |=1<<(BITNUM)))
#define CLRBIT(REG,BITNUM)   ((void) (REG &= ~(1<<(BITNUM))))

//create prototypes for SPI
void spi_int(void);
unsigned char isBusy(void);
unsigned char readStatusRegister(void);


//create variables for SPI
unsigned  char junk;       //variable used to interface with flash
unsigned  char flashByte;  //variable used to interface with flash

int AT=0; //set to fsacnf to varify sending data

//set up SPI for the flash memory********************************************

void spi_int(){ 
  
//Data Directional Register
	SETBIT(DDRB, 7);  //SCLK  to output
	CLRBIT(DDRB, 6);  //MISO  to input
	SETBIT(DDRB, 5);  //MOSI  to output
	SETBIT(DDRB, 4);  // Chip Select
	SETBIT(PORTB,4);

//Set up SPCR
	CLRBIT(SPCR, 7);  //disable interrupts
	SETBIT(SPCR, 6);  //SPE - enable
	CLRBIT(SPCR, 5);  //DORD msb (most sig bit)first
	SETBIT(SPCR, 4);  //MSTR - set uc (micro) as master
	CLRBIT(SPCR, 3);  //CLOCK PHASE/POLARITY
	CLRBIT(SPCR, 2);  //Mode 0
	CLRBIT(SPCR, 1);  //SPCR=SPR1<<0, for fck/16
	SETBIT(SPCR, 0);  //SPCR=SPR0<<1, for fck/16

//Set up SPSR
	SPSR=0x00;  //overclock bit; speed 1/16

  } //end spi_int

//***************************************************************************
//Read Status Register
unsigned char readStatusRegister() {
  
	CLRBIT(PORTB, 4);  //Select Chip
	SPDR = 0xD7;  		//this is the 'read status' command
	while(!(SPSR & (1<<SPIF)));  //polling the SPI Interrupt Flag (SPIF)
	junk  = SPDR;  		//read Data Register
	SPDR = junk;  		//causes 'junk' to be written
	while(!(SPSR & (1<<SPIF)));  //polling the SPI Interrupt Flag (SPIF)
	flashByte = SPDR;
	SETBIT(PORTB, 4);  //  de-select chip
	return flashByte;
  }// end readStatusRegister	

//***************************************************************************
//  is flash memory busy?
//  The seventh bit of the Status Register is "not busy"
unsigned char isBusy(){
	return !(readStatusRegister()>>7);
  }//end isBusy

//***************************************************************************

//variables for buffer
unsigned int byte = 0;  //write to buffer, byte starting at '0' within the buffer

//variables for memory
unsigned int page = 0;  //write to memory, page starting at '0' within the memory

//variables used to store in-coming matlab values
unsigned int n = 4; //this is the length of from_matlab[]
unsigned int from_matlab[4];	//value coming from matlab

int main(void)
   {		
	//set up the ports
	DDRA=0x01;
	DDRB=0xa8;
	DDRC=0x00;
	DDRD |= 0b00110000;  //data directional register for portD for LED D4=green and D5=yellow
 
	spi_int();     //initialize SPI for flash memory
	
	initialize();  //initialize uart
	
		//*************************blink to verify initialized
		PORTD |= (LED_D5);
		_delay_us(500000);
		PORTD &= ~(LED_D5);
		//*************************
	
   
	while(1)
       {
			
	  AT=fscanf(stdin, "%d", &from_matlab[1]);//received value from matlab
		
		if(AT==1){	
		//*************************blink to verify received from matlab
		PORTD |= (LED_D4);
		_delay_us(50);
		PORTD &= ~(LED_D4);
		//*************************
	}
			
	while(isBusy());
		
//************[START]********send to 1284p buffer*****************************************

	//write to Buffer in 1284p
  
	// Write 'n' bytes to buffer
	// opcode 84H (87H for buffer 2) 
	// 3 addr bytes: 10 'Don't Care', 10 buffer addr bytes
	// then can send data
	
	unsigned char opcode_Buf = 0x00;
	
	opcode_Buf = 0x84;  //84H is buffer 1
		
	unsigned char message_Buf[4] =
			{opcode_Buf,		//  opcode
			0x00,			//  'Don't Care' bytes
			(char)  (byte>>8),	//  [2 'Don't Care bytes; BA9-BA8
			(char)  (byte)};	//  [BA7 - BA0]
					
	CLRBIT(PORTB,4);  			//  Select Chip
	
	//***starts sending BYTES over SPI***
	for  (int k=0; k<4; k++){
		SPDR = message_Buf[k];
		while(!(SPSR & (1<<SPIF))); //causes 'wait until complete'
		junk = SPDR;  // prompts 'read Data Register'
	}

	//***Now, start sending DATA over SPI***
	for (int k=0; k<n; k++){
		SPDR = from_matlab[k];//assuming that the RIGHTSIDE of SPDR is in-coming data from matlab
		while(!(SPSR & (1<<SPIF))); //causes 'wait until complete'
		junk = SPDR;  // prompts 'read Data Register'
		}
		
	SETBIT(PORTB, 4);  //de-select chip
		
//************[end]********send to 1284p buffer*******************************************

		while(isBusy());
		
//************[START]********send to 1284p from buffer to main memory*********************		
	//write main memory for buffer (with or without built-in erase)
	// send data from matlab, from 1284p buffer to 1284p main Memory
	//  Built-in erase: opcode 83H (86H for buffer 2)
	//  No erase: opcode 88H (89H for buffer 2)
	//   3 addr; 1 'Don't Care' byte, 13 page address, 10 'Don't Care' bytes
		
	unsigned char opcode_Main = 0x00;  //declare and initially assign opcode
		
	opcode_Main = 0x83;//buffer 1, built-in erase
				
	unsigned char message_Main[4] = 
		{opcode_Main,		//  opcode
		(char) (page>>6),	//  ['Don't Care' byte, PA12-PA6]
		(char) (page<<2),	//  [PA5-PA0 2DC]
		0x00};			//  'Don't Care'
		
	CLRBIT(PORTB, 4);  //  select chip	
	
	//start sending BYTES over SPI
	for(int k=0; k<4; k++){
		SPDR = message_Main[k];
		while(!(SPSR & (1<<SPIF))); //causes 'wait until complete'
		junk = SPDR;  // prompts 'read Data Register'
		}
	
	SETBIT(PORTB, 4);  //de-select chip
		
//************[END]********send to 1284p from buffer to main memory***********************
				
	}//end while(1)
  	
  }  //end 'main'