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Unable to flash nRF9160 with "ninja flash"

I'm building some of the samples using command line in Ubuntu and have a strange issue. Everything builds fine, the merged.hex file is generated, however when I try to flash the device using "ninja flash" the boot loader never runs the application:

SPM: MSP_NS 20023088
SPM: prepare to jump to Non-Secure image

However the following all work:

1. Flashing the image using J-FlashLite

2. nrfjprog -e; nrfjprof --program merged.hex

3. nrfjprog -e; ninja flash

SPM: MSP_NS 200236c8
SPM: prepare to jump to Non-Secure image
***** Booting Zephyr OS 1.14.99 *****
The AT host sample started

Does anyone know what the issue might be here? Is ninja flash corrupting something during the erase?

For some reason I am currently unable to reply to the below posts so I'm adding this here:

$ nrfjprog -v
nrfjprog version: 10.1.1
JLinkARM.dll version: 6.46g

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