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How do you put it in alphabetical order using code? Everything I've read says to delete this value:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu\&Programs\Menu\Order
Even though I've done that it still doesn't alphabetize it, even after restarting the computer.
Maybe this will throw some light on it.
In MSDN, the following functions: RegEnumKeyEx, and RegEnumValue, both state that
'they [either of the above] are not ordered, any new value will have an arbitrary index.'
This means even at an API level you cannot control the ordering of values, or keys in the registry.
I'm not sure how relevant this is to the start menu, but it may be of some help.