First clean up the Unchecked items that you want to permanently get rid of.
Start>Run, key in Regedit and press enter. In the left pane click on HKEY_Local_Machine\Software\Microsoft\Windows\ CurrentVersion\Run-
Now in the right pane, do you see the entry listed in the "Run-" key. Not the "Run" key but the "Run-" key. If so, right click on it and select delete.
Now do the same for the following locations
HKEY_Local_Machine\Software\Microsoft\Windows\ CurrentVersion\RunServices-
HKEY_Current_User\Software\Microsoft\Windows\ CurrentVersion\Run-
Now check the "Disabled Startup Items" folder.
Start>Search>Files, key in Disable* and press enter. Now locate the "Disabled Startup items" folder and double left click on it to Explore it. If you see any items there that you want to permenantly get rid of, delete the shortcut from that folder.
Now rerun Msconfig. Did it get rid of all of the unchecked items your looking to get rid of?
Let us know what happens.