Using Ubuntu (same behavior on 20.04, 22.04, and 22.10) and nRF Connect for Desktop 3.12.0. I have my J-Link hooked up to an nRF9160 on a custom board. When I check it at the command line, everything looks good:
me@computer:~$ nrfjprog --version nrfjprog version: 10.18.1 external JLinkARM.dll version: 7.82b me@computer:~$ nrfjprog -i 261008254 me@computer:~$ nrfjprog --deviceversion NRF9160_xxAA_REV2
The Segger software works great - JFlash, JLinkConfig, etc. But none of the nRF Connect apps see my J-Link. I have "Show only supported devices" unchecked:

But no device:

No idea where to go from here. It typically works fine.