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Moving from pca10056 to pca10059, unable to debug in Segger Embedded Studio

I'm moving a project from pca10056 to pca10059.   When programming the pca10059 via the JLink Edu Programmer, the application uploads fine, however it hangs entering debug and doesn't execute the program when using Segger Embedded Studio.

If I take the same application hex and S140 soft device and program it via nRF Connect programmer via the usb booitloader, then if I connect it upto Segger via JLink in Segger Embedded Studio, it can then debug fine.

I.E. Exact same application hex and soft device with both approaches.

Doing a read of the device programmed both ways with:  ./nrfjprog -f nrf52 --memrd 0x00000000 --n 0x100000  and comparing them, the only difference is in the boatloader settings:

< 0x000FF000: A97F6AE7 00000001 FFFFFFFF 00000003 |.j..............|
< 0x000FF010: 00000000  00000001 00023C78 C9D3B62E   |........x<......|
---
> 0x000FF000: 4AF7B8F3 00000001 FFFFFFFF 00000003   |...J............|
> 0x000FF010: 00000000 00000001 00023C78 83AC440A   |........x<...D..|
So I suspect segger isn't programming the same boot loader settings, but I haven't found a setting in segger that changes the bootloader settings.
Any ideas on how to get segger to upload code where the JLink Debugger can be used on the pca10059 from within Segger?
Thanks
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