Isn't that weird? You have to edit your regedit to resolve the issue. I'm writing the working solution from the thread http://en.kioskea.net/forum/affich-21376-not-showing-hidden-files-and-folders, so that you don't need to read all of them.
o Open registry( select run command from start menu and type regedit and then press enter)
o In the left pane goto path HKEY_LOCAL_MACHINESoftware\Microsoft \Windows \CurrentVersion \Explorer \Advanced \Folder \Hidden \SHOWALL
o Delete the value CheckedValue in the Right pane by right clicking it and selecting delete. (Its type should be REG_SZ and data should be 2.)
o Create a new DWORD value called CheckedValue by right clicking in the Right pane and then selecting new -> DWORD Value and then changing the name to CheckedValue. (same as above, except that the type is REG_DWORD). Modify the value data to 1 (0Ã—00000001) by right clicking the CheckedValue in the Right pane and selecting modify and changing the value data to 1.
Hope the little solution will work for you. But I'll advice you to update your Anti-Virus, and do regular scanning on your PC. The problem was happened due to virus attack, and probably you won't want to affected once again. So be careful yourself.