The issue is that TDL will only find the preferences if they are called 'ToDoList.ini'.
So the fix is to NOT show the subsequent 'Do you want to start using...' message unless this is the case.
ps. If you save to another filename then the only way to have TDL use these preferences is via the '-i' commandline switch.
pps. Can you confirm that if you save to 'ToDoList.ini' then the preference are correctly reloaded?