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What is the extra information in my .HEX file?

Background:
I'm a noob. I'm attempting to add the ability to update the application on a NXP LPC2468 by using the USB and adding a bootloader. It sort of works. The unit has an LCD and a keypad. A very minor change to the main application will work without any problem. But for instance, if I add a character to a menu, it will cause a problem: The text for the rest of the application will be shifted or entirely wrong.

The bootloader and the USB driver is located in sectors 0-8 in the Flash. The main application is located in Sectors 9-20. When a USB drive with a correctly named .HEX file is connected, the bootloader will erase sectors 9-20, then load the new main application .HEX from the USB.

When comparing Hex files I can see the problem, but I don't know what it is. If I change an existing character lets say a "1" to a "2", I can see the corresponding value in the .HEX change from "0x31" to "0x32" just as it should. If i then remove that character things in the bootloader section will change. I think this is because the "lookup table" for the text is located here? also the area containing the text seems to be randomly pieced together like the compiler optimizes the locations to save memory. When removing a character this area gets changed quite alot.

Also I can see the now incorrect text in the on chip RAM. The IAP commands if i understand them correctly are only for the flash. How do I update the RAM after a USB upload?

Also the part of the .HEX that changes is not part of my code, at least it is not represented in the MAP file. I don't know what it is.

I'm sure I have alot of ignorance about the inner functions of the processor and the compiler. If fact I don't know even what to search for!

Please help!

Thanks,

Todd