There are millions of reasons or possiblities that the files be gone. Even if you have an antivirus software it is very easy for a virus to infect you computer. Also hackers can delete the files if they wanted.
For a simple check if any background software is running that is suspicious go to
start->run-> type in "regedit"
When regedit opens
HKEY_LOCAL_MACHINE -> Software -> Microsoft -> windows -> CurrentVersion -> Run
If you find any file to be suspicious delete it.
I highly recommand that if you are not famliar with regedit you shouldn't delete anything though.
Also try checking RunOnce.