Some ancient versions of the bootloader run at 9600 baud (instead of 19200). In order to successfully upload sketches to boards with this bootloader, you'll need to change the serial.download_rate in your preferences file to 9600.
The "Burn Bootloader" commands in the Arduino environment use an open-source tool, avrdude. There are four steps: unlocking the bootloader section of the chip, setting the fuses on the chip, uploading the bootloader code to the chip, and locking the bootloader section of the chip. These are controlled by a number of preferences in the Arduino preferences file.
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If I try to re-program the protected bootloader with Segger J-Link (both in CodeWarrior and Eclipse/KDS with GDB), then the download silently fails. The effect is that somehow the application on the board does not match what it should be. Looking at the Console view, it shows that erase has failed (but no real error reported) :-(: 2ff7e9595c
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