The way they get added twice is this. If you use Msconfig to disable certain programs that have their own built in options for running at Startup, you will end up with more than one entry since they immediately re-add themselves after you disable them. Sometimes not until after a restart and/or an execution of that particular program. To get rid of most of them you need to delete the registry entries, obviously leaving one for each program so they still run at startup. To stop this from happening, if you want to disable them, go into the program and use the options in it to disable them rather than Msconfig. The registry entries can be found here, Start>Run,key in Regedit and press enter. Double left click on each entry in the left pane. After you've double left clicked on Run in the left pane you will see the startup entries in the right pane.
HKEY_Local_Machine>Software>Microsoft>Windows>CurrentVersion>Run
HKEY_Local_Machine>Software>Microsoft>Windows>CurrentVersion>RunServices
Just right click on an entry in the right pane and select Delete to remove the duplicate entries that are selected to run at startup from the Run section.
Or delete any entries in here, which will be the Disabled duplicate entries you're seeing in msconfig.
HKEY_Local_Machine>Software>Microsoft>Windows>CurrentVersion>Run-
BTW, EaFiedler is correct about the "Disabled Startup Items" folder but that only applies to programs that use a shortcut in the Startup folder to run at Startup. Most nowadays use a registry entry though there are still some common exceptions like MS Office.
The third place to look would be in win.ini for duplicate noload= or load= statements, but they usually don't occur.
Just so you know, Run and RunServives both execute at Startup but at different times. RunServices is what I would describe as a "Machine Level" run. Eccentially prior to Windows having been loaded. And Run tasks are loaded after Windows has loaded but before the GUI is displayed to the user. Good Luck.
Now that I have said all of that, from what I understand, <a href=http://hotfiles.zdnet.com/cgi-bin/texis/swlib/hotfiles/info.html?b=pcm&fcode=000YKL> StartupCop</a> deletes the entries for you and can be used for W95 or W98. At least I've been told it deletes them. You'd have to try it.
[This message has been edited by bhesson (edited 08-24-2000).]