What are you trying to reconfigure? Check out this sight, it may do what you want, but better. http://www.blackviper.com/
geez thats a bit of a bitch that is. Another way to check what runs at startup is through Regedit. Click Start - Run, type Regedit and navigate to HKEY_LOCAL_MACHINE/Software/Microsft/Windows/CurrentVersion/Run You should see a list of string values, these are the programs that run at startup! Are you chasing a virus or trojan by any chance? because they also have sneaky ways of hiding BTW, if u delete any of the value's from RUN in regedit, it wont start at startup, a tap of the F5 key will refresh the registry when you are finished. Also HKEY_CURRENT_USER/Software/Microsoft/Windows/CurrentVersion/Run also has things that start at startup!
Try starting it from a DOS window, open a command prompt and type msconfig or regedit and see if that gives you a clue as to why they are not opening. It might be a file not found or other message that flashes too fast for you to see.
Thats sounds like a virus then. I know the Spybot worm disables regedit, msconfig, and task manager. Check out http://www.sophos.com/virusinfo/analyses/w32spybotbm.html for info on determining if you have it and removal instructions.
Reboot and enter safe mode booting. When cxomputer is booting keep hitting F5 and you will get a list of options, select Safe Mode! Now try using msconfig!
