Re: how to totally get rid of nvidia-settings configurations on login
It seems pretty unlikely that nvidia-settings itself is causing these problems. The .nv directory is not part of nvidia-settings, but is used by OpenGL and is almost certainly unrelated. nvidia-settings doesn't do anything to make itself automatically loaded, so if it's being run, it's happening via something your desktop environment is doing.
One easy experiment to try would be to run "sudo chmod -x /usr/bin/nvidia-settings" to make it not executable. If your problem still occurs, then something else is at fault.