Problem in Flash Programming of PIC24FJ128GC006 - bootloader

Question

I am making a USB Bootloader for PIC24FJ. I am now in the process of writing to flash memory the application code hex file through a software and without using ICD3. After downloading the application code hex file, I checked the program memory of the PIC using the PIC Memory Views of MPLAB Window Toolbar, and this is what it looks like. PIC24_BOOT_APP_VECTOR_AREA As you can see in the picture, the opcode is not continuously written in every address. It alternates with 000000.
Also I compared the opcodes of the downloaded app code using the bootloader, to the application code without using the bootloader. I have found out that there are data in the opcodes that are not present in the application alone. Attached are the photos. Application_Code_Alone_User_Area, PIC24_Boot_App_User_Area This may create a problem in jumping to the application.
Below is my code for storing data in the buffer and writing to flash memory. (I use single word programming for flash)
#define WRITE_FLASH_BLOCK_SIZE 0x04
#define USER_MEM_START_ADDRESS 0x004002
unsigned long rxBuff[60];
int rxIndexer;
int xfer;
lineStart = rxBuff[ 0 ];
positionAddress = (rxBuff[ 2 ] << 8) + (rxBuff[ 3 ]); // THIS IS THE ADDRESS WHERE THE DATA SHOULD BE ADDRESSED
numberOfData = rxBuff[ 1 ]; // THIS IS THE TOTAL NUMBER OF DATA RECEIVED IN THE STREAM
recordType = rxBuff[ 4 ];
rxIndexer = 5; //Start of data index in a INTEL Hex file format
for(xfer = 0; xfer < numberOfData; xfer += WRITE_FLASH_BLOCK_SIZE) // THIS SECTION CONTAINS THE PROCESS OF COMBINING THE INFORMATION
{ // FROM THE DATA STREAM TO THIS FORMAT - 0x00AA, 0xBBCC
rxBuff[rxIndexer] = ((rxBuff[START_OF_DATA_INDEX + xfer]) &0x00FF);
rxBuff[rxIndexer] |= ((rxBuff[START_OF_DATA_INDEX + xfer + 1] << 8) &0xFF00); //end of lower word
rxIndexer++;
rxBuff[rxIndexer] = ((rxBuff[START_OF_DATA_INDEX + xfer + 2]) &0x00FF); //start of upper byte
rxBuff[rxIndexer] |= ((0x00 << 8) & 0xFF00); // phantom byte (0x00)
rxIndexer++;
}
if(lineStart == ':')
{
if(recordType == 0x00 && data_checksum == 0)
{
for(xfer = 0; xfer < numberOfData; xfer += 2)
{
FlashWrite_Word(programAddress + positionAddress, rxBuff[5 + xfer], rxBuff[5 + xfer + 1]);
positionAddress += 2;
}
}
else if(recordType == 0x04 && data_checksum == 0)
{
programAddress = USER_MEM_START_ADDRESS;
}
else if( recordType == END_OF_FILE_RECORD)
{
jumpTo_App();
}