Running Win7. The Start Menu was getting too big, so I've navigated to C:\ProgramData\Microsoft\Windows\Start Menu\Programs and created some sub-folders in various categories [image editors, system utilities, media players, security for example] in which to group the shortcuts. Having created the group folders, I've dragged and dropped the Start Menu shortcuts into them.

However it seems all Start Menu shortcuts are not alike.

1. Some programs, their shortcut folders having been moved from the Start Menu, spawn NEW [but empty] folders bearing their company names in the top level of the Start Menu eg AVICodec

2. Some programs don't have Start Menu shortcut folders that can be seen in WinExplorer [or equiv] at all, even though they turn up under the Start Menu itself. It seems these can be moved where they are visible i.e. in the Start -> All Programs by dragging and dropping not just onto the desired folder but by hovering to expand the desired folder and then dropping between other shortcuts there. Eg Daum, Format Factory That's not such a problem, but why it's happening is a mystery.

What's going on, and how to make these shortcuts behave normally or otherwise control them properly?