Missing Programs in All Programs Menu

It is possible that a parasite of some sort has caused the issue. You should scan for viruses and adware/malware as a precaution. I recommend the following scanners:

Adaware SE
AVG Anti-Spyware
AVG Virus Scan

To restore your programs to the All Programs menu, try this:

Go to Start>> Run. Type in: regsvr32 /i shell32.dll [Enter] or click OK.

Restart Windows.

Your programs should now be restored to the All Programs menu.