If you find an intermittent issue where the shortcuts on a Windows 7 desktop disappear it is likely because of the automatic maintenance windows does to remove missing shortcuts.
In order to resolve this issue need to disable the automatic maintenance following the procedure below
In Control Panel under System and Security go to Find and fix problems
on the menu on the left choose change settings
Set Computer maintenance to off
Information from http://support.microsoft.com/kb/978980/en-us?p=1