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TMS320F28335PGFA Boot loader SCI won’t run after reset



We have written a boot loader to download FLASH using the API.  So I down load the loader through serial. I erase flash then I program flash and checksum the flash everything looks correct I then reset the processor nothing happens. I have logged out the contents of flash and compared it with what I downloaded through JTAG they are the same I have re-read the flash with the debugger to prove the contents are the same. Is their some address or register that I also have to rite to that is being written to by the debugger?