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.