This
might be it. There is a registry value "noinstrumentation" which disables tracking of items for the start menu. Then, only items that you drag and drop there will appear. Actually, it's something I've always done with my windows installs, so I don't get a load of crappy non-matching icons screwing up my mods.
Open your registry and find the key below:
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer
Create, or modify, the DWORD value "NoInstrumentation" and set the value to "0" to disable the restriction.