But where? I've done some investigation and i'm lost here.
I can reproduce it consistently pressing restart but i don't know where the problem is. Some food for thought: after pressing restart several times i can see the config has been reset at the iwad selection startup window. You can see that easily selecting another backend different from the default one and saving the config earlier. Then i've noticed that when you press exit in the picker the config is not saved so when i see that the settings have been reset and exit the config file is not overriden. If i restart again of course i lose my config file.
With my code (but it's the same in GZDoom) i can see putting a Printf that the file is opened succesfully and the succ variable is true every time even when the config is reset. If i remove the read permission from the file before restarting i get the "Could not open config file error message". And it's not something related to saving since i exit without saving and i never get the dialog with the "configuration not saved" error.
void FConfigFile::LoadConfigFile ()
FileExisted = FileExists(PathName.GetChars());
if (!file.OpenFile (PathName))
I_Error ("Could not open config file.\n");
succ = ReadConfig (&file);
FileExisted = succ;