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Bootloader and settings problem - gcc compiler

I have a custom board with an application that works fine. 

But when adding a secure bootloader my board starts to act weird. I am using the RESET pin on the chip as an input PIN. My chip resets every time the input is used when the app is run with the bootloader. But it works fine without the bootloader.

I am running SDK13 - Softdevice 4.0.5 on a nrf52832CIAA. 

I am compiling with gcc - both the app and bootloader. I have used nrfutil to create bootloader settings file. 

I have used merge-hex to merge the SD, app, Bootloader and settings-file.

All has been run on a MAC / OSX.

I have read somewhere on the Nordic DEVZONE that the gcc compiler places the settingsfile in the wrong place of the memory map. But I lack a good method of fixing it.

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