NRF54L15 - issue when MCUBoot/Partition Manager is used on a custom board

Dear Team,
I am experiencing a weird issue with the firmware on my custom EV board with NRF54L15.
My firmware is using MCUBoot and partition manager (I use a separate flash partition for storage) and it runs just fine on my NRF54L15 DK board.
However, once I program it to the custom board, it just doesn't start.
I have also noticed in NRF Programmer that there is always a difference in memory layouts between File and Application (unfortunately, to some reason it is not allowing me to read the memory from DK board chip). Specifically, after flashing, the application size becomes around 3 kb smaller,9 kb storage partition (in the middle) shrinks to 32 bytes while MBR (orange partition) becomes bigger by approximately the size of the storage partition.
Once I remove MCUBoot and Partition Manager dependencies from my prj.conf, I am able to run the firmware (but obviously, it now won't be able to use storage and MCU Boot).
The firmware gets built for NRF54L15DK board and nrf54l15/cpuapp qualifier. 
What could be the issue?
Thanks
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