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Messages - defib

#1
I'm developping and debugging my LPC1754 board usually via JTAG and the IDE CrossStudio from Rowley.
I implemented my own flashtest with a checksum over the whole used flash memory.
When flashing and debugging with JTAG the flashtest works.
However, when i tried to update the firmware with the on-chip bootloader and Flash Magic, the checksum algorithm always failed.
I discovered, that the 4 bytes "Valid User Code" at 0x1C are different, when i read back and compare the memory content:
When flashed via JTAG, there is always 0x00000000 - when flashed via Bootloader/FlashMagic there is a non-zero entry.

Is it possible to disable in Flash Magic this image modification?
Why does the uC starts at all, when there is a "Valid User Code" of 0x00000000 written via JTAG  ???