flash nrf52832 using command line differs from flashing via segger

Question

Hello all 
 
 currently I am flashing the device using command line: 
 
 #erase chip nrfjprog --family NRF52 --recover #program softdevice nrfjprog --family NRF52 --program .\firmware-img\s132_nrf52_6.1.1_softdevice.hex --chiperase #program bootloader nrfjprog --family NRF52 --program ..
RF5_SDK_15.2.0_9412b96\examples\dfu\secure_bootloader\pca10040_ble\ses\Output\Release\Exe\secure_bootloader_ble_s132_pca10040.hex #program software nrfjprog --family NRF52 --program .\Project-nRF52832\Output\Debug\Exe\BLE-nRF52832.hex #reset chip nrfjprog.exe --family NRF52 --reset 
 
 software uploads, but FOTA process fails 
 
 however, if after that process I flash the application software only via JTAG, then power board on\off, and then performing FOTA all works fine 
 
 this is the output while flashing using segger (notice content already match so no software is being downloaded):, please advice

Preparing target for download
Executing script TargetInterface.resetAndStop()
Reset: Halt core after reset via DEMCR.VC_CORERESET.
Reset: Reset device via AIRCR.SYSRESETREQ.
Downloading ‘s132_nrf52_6.1.0_softdevice.hex’ to J-Link
Programming 2.3 KB of addresses 00000000 — 00000967
Programming 144.8 KB of addresses 00001000 — 0002536b
J-Link: Flash download: Bank 0 @ 0x00000000: Skipped. Contents already match
Download successful
Downloading ‘BLE-nRF52832.elf’ to J-Link
Programming 67.0 KB of addresses 00026000 — 00036c2f
Programming 0.0 KB of addresses 00036c30 — 00036c33
Programming 0.0 KB of addresses 00036c34 — 00036c47
Programming 11.2 KB of .rodata addresses 00036c48 — 0003996f
Programming 0.1 KB of addresses 00039970 — 00039a33
J-Link: Flash download: Bank 0 @ 0x00000000: 1 range affected (4096 bytes)
J-Link: Flash download: Total time needed: 0.391s (Prepare: 0.126s, Compare: 0.069s, Erase: 0.031s, Program: 0.071s, Verify: 0.001s, Restore: 0.089s)
Download successful
Connecting ‘J-Link’ using ‘USB’
Connecting to target using SWD
Loaded C:/Program Files/SEGGER/SEGGER Embedded Studio for ARM 4.12/bin/JLink_x64.dll
Firmware Version: J-Link OB-SAM3U128-V2-NordicSemi compiled Jan 7 2019 14:07:15
DLL Version: 6.40`
Hardware Version: V1.00
Target Voltage: 3.300
Device "NRF52832_XXAA" selected.
Found SW-DP with ID 0x2BA01477
Found SW-DP with ID 0x2BA01477
Scanning AP map to find all available APs
AP[2]: Stopped AP scan as end of AP map has been reached
AP[0]: AHB-AP (IDR: 0x24770011)
AP[1]: JTAG-AP (IDR: 0x02880000)
Iterating through AP map to find AHB-AP to use
AP[0]: Core found
AP[0]: AHB-AP ROM base: 0xE00FF000
CPUID register: 0x410FC241. Implementer code: 0x41 (ARM)
Found Cortex-M4 r0p1, Little endian.
FPUnit: 6 code (BP) slots and 2 literal slots
CoreSight components:
ROMTbl[0] @ E00FF000
ROMTbl[0][0]: E000E000, CID: B105E00D, PID: 000BB00C SCS-M7
ROMTbl[0][1]: E0001000, CID: B105E00D, PID: 003BB002 DWT
ROMTbl[0][2]: E0002000, CID: B105E00D, PID: 002BB003 FPB
ROMTbl[0][3]: E0000000, CID: B105E00D, PID: 003BB001 ITM
ROMTbl[0][4]: E0040000, CID: B105900D, PID: 000BB9A1 TPIU
ROMTbl[0][5]: E0041000, CID: B105900D, PID: 000BB925 ETM
Preparing target for download
Executing script TargetInterface.resetAndStop()
Reset: Halt core after reset via DEMCR.VC_CORERESET.
Reset: Reset device via AIRCR.SYSRESETREQ.
Downloading ‘s132_nrf52_6.1.0_softdevice.hex’ to J-Link
Programming 2.3 KB of addresses 00000000 — 00000967
Programming 144.8 KB of addresses 00001000 — 0002536b
J-Link: Flash download: Bank 0 @ 0x00000000: Skipped. Contents already match
Download successful
Downloading ‘BLE-nRF52832.elf’ to J-Link
Programming 67.0 KB of addresses 00026000 — 00036c2f
Programming 0.0 KB of addresses 00036c30 — 00036c33
Programming 0.0 KB of addresses 00036c34 — 00036c47
Programming 11.2 KB of .rodata addresses 00036c48 — 0003996f
Programming 0.1 KB of addresses 00039970 — 00039a33
J-Link: Flash download: Bank 0 @ 0x00000000: Skipped. Contents already match
Download successful