There exists a very serious and critical BUG in Startup Manager
After disabling an item, rebooting, enabling that item again and rebooting, the item's registry entries are gone from the registry.
Even without rebooting the BUG appears: you have only to close Startup Manager and open it again after disabling and after enabling!
So the users risk some programs not starting up anymore at boottime without possibility to recover the situation.
Please read very carefully this thread
Notice: this happens in Vista Ultimate 32-bit