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Buttons and LED's does not work

I have developed software for a custom board (#1) with the nrf52832-CIAA (QFN packet) with LED's and buttons. It works.

I use the same software for another custom board (#2) with the nrf52832-CIAA (BGA packet) with LED's and buttons. It does NOT work. No LED or Button is working. The #2 board is advertising - I can connect, etc. 

I have changed the corresponding logical I/O's to match #2 in my custom_boards.h file.

I am using the same Softdevice for both boards.

Could you please advice me on what to look. 

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