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ELF produced binary code vs. JTAG uploaded code

Anyone know why the binary code generated by the Keil ELF tool is different from the JTAG uploaded code? It looks like the last 150 bytes or so are different. I have a automatic firmware update tool that occasionally fails to restart. I have noticed that as my code size gets close to the size boundary (within 4000 bytes or so), the update fails to restart almost all the time (and won't work until I reload from JTAG). I've then noticed that the JTAG uploads different code than the ELF tool produces. What is the difference?