Presumably you're talking about the startup tab in msconfig?
This is something which is not very satisfactory with msconfig. When you disable an item, the registry entry is removed, but in msconfig itself the old box is still there (so that you can re-enable it).
But something (like using a program, reinstalling, or updating driver) can write another entry to the registry and a new box with the same name will appear, reflecting what is in the registry, giving you double or multiple entries.
You can't delete it directly from msconfig. The only way I know of is to tick the box, so that the entry will reappear in the registry itself, then use regedit to manually delete the entry. Then the box won't show in msconfig.
What I suggest you do is use another startup manager, such as Mike Lin's Startup Control Panel 2.8 click here and install it. Go to Control Panel, Startup icon, and you can go through each tab to see the startup items. You can disable an item by unticking it. If the item is re-created by the application, you will still get a duplicate box, but you can right click the duplicate box and delete it. It will then be sent to the Deleted tab, where you can permanently remove it.
If you still want to remove the duplicate boxes in msconfig, post back, but you will have to use regedit.