Programs missing in Start Menu and admin permission lost

Please see both of these articles:
Temporary connection-related errors may occur when you use Windows Update or Microsoft Update

How to troubleshoot problems connecting to Windows Update or to Microsoft Update

Are you the Administrator of this computer? I see you as a /user/

Got some questions for you:

1. How did you install Windows 7, upgrade or clean install?
2. Did you install any update before you encountered this issue?

Let's also see if flushing the DNS cache and restoring MS's Hosts File works--->
Copy and paste these lines in Note pad.

@Echo on
pushd\windows\system32\drivers\etc
attrib -h -s -r hosts
echo 127.0.0.1 localhost>HOSTS
attrib +r +h +s hosts
popd
ipconfig /release
ipconfig /renew
ipconfig /flushdns
netsh winsock reset all
netsh int ip reset all
shutdown -r -t 1
del %0

Save as flush.bat to your desktop.
Double click on the flush.bat file to run it.Vista and Windows 7... right click the .bat file and choose to run as Administrator. Your computer will reboot itself.

I see you as a /user/ ... were you ever the Administrator?

Also can you answer my other questions?

1. How did you install Windows 7, upgrade or clean install?
2. Did you install any update before you encountered this issue?

Just a thought...

Are apps not running because UAC is disabled?

On the Administrator/Permissions lost issue, is it possible to do this, or do you get a 'no go'...

Start > All > Programs > Accessories > Command Prompt
Right-click the Command Prompt and select: Run as Administrator

Copy/paste the entire text in the code box, and paste it at the blinking cursor of the Command Prompt:

Code:

 
reg query "HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies\system" /s >look.txt
start notepad look.txt
exit

Do you get any results titled look.txt?