I think I might have located something in the latest v2.4.0 and v2.4.1 SDKs that others might run into, it involves using mcuboot while also using an SD card (on spi3) in the application.
If this is a repeat post then I apologize, I have not fully searched the forums here yet.
I turns out that a new option has been added to mcuboot in v2.4.0 (Zephyr v3.3.99) (CONFIG_SPI_NOR=y) which conflicts with spi3 in the application. Adding CONFIG_SPI_NOR=y to the mcuboot prj.conf will resolve the issue. I made the following post on Nordic’s forums and would like to provide that information here as a heads up.
I am waiting for a reply from Nordic currently, but the above work around appears to be ok for now (as long as external NOR is not needed if using mcuboot for FOTA updates).
See the below post for a clean way to add the mcuboot options to the project without altering the SDK.
https://devzone.nordicsemi.com/f/nordic-q-a/102609/nrf9160-enabling-mcuboot-in-v2-4-0-causes-sd-card-on-spi3-to-stop-working-spi3-conflict
Allan