there are about a dozen places in the registry were they are stored, not just those two. Get something like autoruns from sysinternals.com and you can all edit them comfortably. It also lists the registry keys for all of them
You forgot "Windows" after Microsoft...
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnceEx
#2 and 3 I don't believe start up automatically, I think they just define what programs should be copied into the startup entries of new user accounts.
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