I tried to upgrade the modem firmware on NRF9160-DK to the latest 1.3.0, downloaded from https://www.nordicsemi.com/Products/nRF9160/Download#infotabs.
After (succesfull) upgrade, the modem initialization fails (hangs for a long time and returns with errors) on nrf_modem_init().
When reverting to 1.1.0, everything works fine again. Also, upgrading to 1.1.1 works fine, so it's not like it's impossible to upgrade the modem.
On another custom board, I can correctly use the 1.3.0. Maybe there is a hw-rev dependency? If so, maybe those dependencies could be listed and checked automatically in the programmer tool? The NRF9160-DK is using NRF9160_xxAA_REV1, whereas the custom board is using NRF9160_xxAA_REV2.