I use an AutoHotkey script to handle startup. Be warned that it clears any current entries in the registry and startup folder. First it asks if you want to run startup apps (all or nothing). Then it loops though a customizable startup folder (on my machine... D:\_Links\Startup) launching all shortcuts. I do this to ensure that one place controls all my startup apps. I also have FARR indexing the same folder to launch any of the same apps after startup.
#SingleInstance FORCE
MsgBox, 4, AutoHotkey Start, Whould like to run startup apps?, 10
IfMsgBox, No
return
;;; Clean reg
RegDelete, HKCU, SOFTWARE\Microsoft\Windows\CurrentVersion\Run
RegDelete, HKLM, Software\Microsoft\Windows\CurrentVersion\Run
RegWrite, REG_SZ, HKCU, Software\Microsoft\Windows\CurrentVersion\Run, Start, %A_ScriptFullPath%
;;; Clean start menu
FileDelete, %A_StartMenuCommon%\Programs\Startup\*.*
FileDelete, %A_StartMenu%\Programs\Startup\*.*
;;; Open apps
Loop, D:\_Links\Startup\*.lnk
{
Run, %A_LoopFileFullPath%
}