I take it you are talking about duplicate entries when using the "Startup"
tab in msconfig?
If they are truly duplicates, either way, you have to edit the registry or
remove programs from Startup folder.
may want to backup registry before editing .
There are various way entries are put in Msconfig. Some come from programs
in your Start>Programs>Start up folder. Some of the entries can be removed by
removing program from this folder. This will remove them from registry. It is
the easiest way to alter registry and less risk involved.
