Are the files actually missing or are they hidden ? There are several types of rogue antivirus/adware type programmes that do that
To determine this run Rogue killer and select the shortcuts fix option
[*] Download RogueKiller and save it on your desktop.
NOTE: If using IE8 or better Smartscreen Filter will need to be disabled
[*]Quit all programs
[*] Start RogueKiller.exe.
[*] Wait until Prescan has finished …
[*] Click on Scan
https://dl.dropbox.com/u/73555776/RKScan.GIF
[*]Wait for the end of the scan.
[*] The report has been created on the desktop.
[*] Click on the Delete button.
https://dl.dropbox.com/u/73555776/RKDelete.GIF
[*]The report has been created on the desktop.
[*]Next click on the ShortcutsFix
https://dl.dropbox.com/u/73555776/RKFixShortcuts.GIF
[*]The report has been created on the desktop.
Please attach: All RKreport.txt text files located on your desktop.