In msconfig, when exactly do the "services" and "startup" items get run? Do the services run on boot, and do the startup items run when the user logs in? Also do the startup items get started up for all users?
Services run at (or near) boot - depending on the startup mode "at startup" or "delayed startup".
MSConfig combines the "All users" and the "logged in user" portions of the startup items (Startup folders and reg keys) into a single list. So the list you see will be different than that of another user.