The problem is solved. Preferences are now being saved properly through application restarts. Except for window position and size for some reason… thinking this is part of Jaikoz.
By the way, that only details running/starting from command-line with ./jaikoz; my problem eventually lay with trying to map the desktop shortcut properly - because the desktop shortcut I created called to execute the wrong executable. I had the Exec path set to execute the .sh file that is in the installation files, which ran the program, but some weird sandboxed version. It was like the application didn’t know where anything (preferences) was because it was only using the rules and references which were defined in the .sh executable.
The only reason I created the shorcut that way is because that is the only way I was instructed to do the same for a different application because there was no other information available regarding creating a desktop shortcut for the application… In fact, I believe it was SongKong…?
TLDR: Preferences weren’t being saved because the wrong executable (jaikoz.sh)was being called in the desktop shortcut which was created to run Jaikoz. Once I changed the Exec path to /home/USER/jaikoz/bin/jaikoz, the topic issue went away.
New Desktop Entry for Jaikoz shortcut - preferences will save and app runs properly:
[Desktop Entry]
Name=jaikoz
Path=/home/USER/jaikoz
Icon=/home/USER/jaikoz/lib/jaikoz.png
Exec=/home/USER/jaikoz/bin/jaikoz
Terminal=false
Type=Application
Categories=Audio;Video;Player;Organization;Music
Keywords=Player;Capture;Audio;Video;Server;Music;Organize