NOTE: it is generally not a good idea to mess around in SCU (unless you are an advanced user), as you could end up messing up your computer as I have once already. I had to do a format of my main HD . I would recommend creating a restore point first :grinthumb .
disabling startup items hardly messes your comp up so bad you need a reinstall. Only thing you can do is to disable some critical service (that's why we have a services tweak guide here).
It is just common sense to make a restore point before you make ANY congifuration changes. You should also make a note of anything you change, so if you do screw up, it will be easy to fix. Nods is right, screwing something up in startup shouldn't warrant a reinstall.
In my case it was as I had numerous registry problems to start with , I must admit that I exaggerated a little bit; I had needed a format anyway. But it can still cause a few unnecessary headaches!
Shouldn't be much probelm dealing with "msconfig". You should see several useful guides in the "Techspot Guides" http://www.techspot.com/guides-os.shtml in assisting you to configure your start-up programs.