I use nRFgo Studio(v.188.8.131.52 win7 x64) "Program Application" to program the combined file(SD+Bootloader+application), it will indicate an error as the attachment. The problem could be seen on all 52840 chip. However, it's ok if I use command line to program it.
But for some 52840 chips, when I use nrfjprog to program, it couldn't program and stop at "Initialzing the QSPI peripheral". I have erase all before programing. These chips couldn't use nRFgo to program, too.
Is this on the nRF52840 PDK? Have you disconnected the external flash memory? If you do not have this memory on you board, you can set MemSize = 0x000000 in C:\Program Files (x86)\Nordic Semiconductor\nrf5x\bin\QspiDefault.ini to prevent nrfjprog from trying to erasing the flash.
MemSize = 0x000000
C:\Program Files (x86)\Nordic Semiconductor\nrf5x\bin\QspiDefault.ini