MSCONFIG from Windows XP (5.1.2600) works correctly on Windows 2000.
MSCONFIG from Windows ME also works correctly on Windows 98 and 98SE, but usually Windows 98 includes it's own MSCONFIG that doesn't have support for things like System Restore.
Also, no version of MSCONFIG works on any version of Windows 95 or Windows NT.
I honestly don't recommend using MSCONFIG at all. The only good thing feature of MSCONFIG that isn't included in other utilities is the ability in Windows 2000 and Windows XP to see Services that are not of Microsoft origin.
If you want to use MSCONFIG to do things like disabling startup items, you should be using something like SysInternals AutoRuns, which works in all versions of Windows, from Windows 95 to XP, and is alot better than 95's SYSEDIT.
http://www.sysinternals.com/files/autoruns.zipIf you use NT, 2000, or XP, you should also see if you have third party device Drivers loaded. These aren't Services or hardware listed in Device Manager. You can find that out using LoadOrder,
http://www.sysinternals.com/files/LOADORD.ZIP.
If you want to enable or disable Drivers, check out L5SG DriverManager, which is free also, available from
http://www.l5sg.com/DriverManager.html.
You have to be very careful removing and adding Drivers to your system, because they often have dependencies that aren't obvious, but, if you are brave, you can find some good tools at
http://www.beyondlogic.org/dddtools/dddtools.htm.
Hope this helps.