Ok nevermind, now it fixed itself (?). But I've noticed that the game insists on reinstalling itself even when closed properly. Upon further tests, it seems that the Itch launcher opens the installation exe instead of the actual software, because when I try to open JRNL from the Itch launcher it installs again resetting my config file, but if I open the exe from the game folder (which for me is C:\Users\[user name]\AppData\Local\Programs\jrnl ) it doesn't reinstall.
Maybe you should find a way to avoid that or talk with Itch customer (?) service to get the proper directory linked?