Windows 7 - Startup programs don't run

Once upon a time I messed with the startup folder locations moving shortcuts from one place to another, and at one time there was a problem with startup programs running twice. Now the problem is, whenever adding a shortcut to the All Programs>Startup folder, the program doesn't run at all, for example the program notepad.

Whenever a shortcut is added to the All Programs>Startup folder,

The shortcut IS visible in the startup folder All Programs>Startup
The shortcut IS visible in C:\Users\(User-Name)\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup

The shortcut IS NOT visible in C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup
The shortcut IS NOT visible in msconfig.

The shortcut DOES NOT run at startup.

I'm running as administrator.

What's going wrong here?

Welcome!

I suggest a repair install.

Thank you, I followed the instructions for repair install (which took 5 1/2 hrs), but the problem persists. Although I'm able to add startup programs with a third party tool (Auslogics Boostspeed), I'd rather fix my Windows 7. Are there any experts here?

Jon is an expert, and one of the best.

I concur.

What happens if you paste the shortcut directly in C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup?

I was asked to provided permission to paste there, but I confirmed it and all went well.

My apologies, please don't take it the wrong way.

Thank you, but when I tried it, something really strange happened. It automatically appeared in the All Programs>Startup menu, however it appeared TWICE in msconfig. When I restarted the computer, the startup program thus started twice. I double checked the C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup folder, and there is only ONE program link. In the C:\Users\(User-Name)\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup folder, there is nothing.

Next, I unchecked one of the duplicate entries in msconfig, restarted the computer, but now the startup program did not start at all! I opened msconfig, and the startup program was now mysteriously changed to a single, unchecked entry. I checked the entry, closed and reopened msconfig, and the startup program was now listed as two checked entries!

This behaviour is baffling. Can anyone help me out with this?

Alright, try adding the program again to C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup.

When you get duplicate entries, look closely in msconfig at them. Expand the Location column, and observe the registry locations they point to.

Are they the same?

Yes, they are the same, but are not registry locations. For example, if I add a shortcut to notepad.exe in C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup, the Location column in msconfig for the duplicate items are both "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup". There are other startup programs in msconfig which were added through the program itself, like Windows Live Messenger, which has a Location of "HKCU\...\Run". Those programs run at startup like normal.

Maybe the problem is that whatever shortcut are added to C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup, it doesn't automatically get added to the registry?