Open L-Edit and select Setup>Application and there you will see the workgroup and user settings for the application. It sounds like you had a workgroup .ini file at one time but the path is now invalid or the ini file is no longer there. You can remove the workgroup setting as that is not needed unless you want to share some basic ini file settings among your workgroup. The user ini file will be needed as that is where your changes to the Setup>Application tab settings will be saved. In v2015.4 update 1 and higher an ledit.ini file will be created automatically here: %appdata%\Tanner EDA\ledit.ini if the user field is left blank. You can create your own ledit.ini file anywhere and point to it in the user field as long as you have write access to that location.
I would suggest creating a new ledit.ini file in the %appdata%\Tanner EDA\ directory if you don't already have one there and point the path to it and that should resolve your issue.