Some of the newer trojans create a registry entry that "hides" the items you're referring to.. They aren't really gone, they're just hidden.. Please download and run the file from the link below:
Clicking on the link below will immediately open a download dialogue window.
Hope this helps.
My AV, TrendMicro Internet Security found a trojan named TROJ Gen.RCIC7km and deleted it. This malware seems to have deleted many of my desktop icons and files. And when I clicked on Start there wasn't any items in the right column, like Control Panel or My Computer, etc. After I restarted the computer in Safe Mode that all came back. When I click on Start and All Programs it lists the programs, but most of the folders are empty. Is there any way to recover lost files and icons? I tried to do a system restore, but it didn't seem to fix anything. I also have a Carbonite account, but I'm not sure that will restore icons and program files. Is the worst case scenario to re-install windows and build everything over again? Help Mr. Wizard!!!!