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Programming and erasing memory changes memory layout and breaks code

Ok so this is an interesting one.

When I got a new PCB with a MDBT42Q module containing NRF52832 I flashed it for the first time (program and softdevice) all the code works perfectly. After that I erase the module with -eraseall command and flashed it again. After that program still works, but my leds on GPIOS 9 and 10 dont work anymore. Erasing & flashing again GPIOS dont do anything.

Checking the memory layout after first flashing and after erasing&flashing the size ist the same, but one bit is on the other place.

On the left is memory of controller after flashing it for the first time and on the right is after erasing&flashing it.

I got no idea what to do/where to look for. 

I am using Eclipse & SDK15.3.

Also how is this type of issue called, English is not my native language.

Thanks for help.

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