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I guess the error comes from the Arduino bootload config/build. But in any case I was not looking to run the Espruino in this way. This is only to show that the bin flashing process works and so there must be a bug in the Espruino bootloader.bin
Otherwise I can't understand why with the Arduino boot loader, Espruino boots correctly.
This will not help, but at least explain restarting. I see reason is RTCWDT_RTC_RESET - that means somewhere in begining watchdog is set up and board was reset by watchdog. I'm not aware of ways to disable a WDT if it was set up (based on expierence from micropython). In micropython, only way to keep your board running is to WDT.feed() the dog if that was set somewhere.