What OS (Windows 7, Vista, XP) are you using?
The symptoms you describe can be indicative of a side effect
from the HDD Defrag family of rogue security programs
which changes file attributes to "hidden", making them appear invisible
so the user thinks some of their files have been deleted. Newer variants of the FakeHDD rogue delete Quick Launch and Start Menu items/folders.
Please download unhide.exe
by Grinler and save to your Desktop. Double-click on the file to run the tool.
After running it, all files will have the "hidden" attribute removed. This includes files that are normally hidden by the operating system and any files you may have intentionally hidden. The tool is designed not to remove hidden attribute for system files. If Quick Launch and the Start Menu were deleted, unhide.exe will attempt to restore them back to their proper location. When done you will need to restore the hidden attributes to those files manually. To do that, open Windows Explorer, go to Tools > Folder Options > View and make that change there.Note: Do not clean out your temporary files/folders until this issue is resolved