Msconfig is a standard system tool in Windows where users can, among other things, disable startup items. It's a great tool if you do not have any other software like Autoruns or Starter in reach that deal with startup programs more efficiently. If you use Msconfig all the time you will notice that deactivated entries will not disappear and that there is no way to delete them permanently from being displayed in the tool.
It would be possible to delete the entry in the Registry because the Registry key where it is located is displayed in Msconfig. If you do not want to fiddle around with your Registry you could use the Msconfig Cleanup Utility which displays all inactive startup entries in Msconfig.
Just check some or all of the entries that you want to permanently remove from the Msconfig dialog.