On the linux version, If there exist a regular file (instead of a dir) called ~/user, the emulator silently fails to save/read its settings
I had this issue for about 2 years, but I wasn't able to find what was causing it until now. Eventually I discovered that the reason was that I had a file named user inside my home dir.
To discover that, I used this command:
strace -f -t -e trace=file dolphin-emu 2>&1
With that I found that the emulator tries to check if there exists a directory ~/user, and if it does exist, it tries to use it to store its settings. However, it seems the emulator does not check if it is indeed a directory or just a plain file.
To replicate this error:
# on a working linux installation of dolphin (where the directory `~/user/` doesn't exist), create a regular file called `user` touch ~/user # btw, if the file `user` is empty or not, doesn't seem to make a difference # at this point, the emulator will not be able to find and store its settings dolphin-emu # to fix it, just remove the `user` file rm ~/user