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First thing I would do is reboot and see if they rebuild. If that doesn't work then do the following:
Right click on Start. Click on Properties. In the Taskbar and Start Menu dialog box click on Customize. Under the general and Advanced tabs you can set your Start Menu options. Then close out by clicking on OK | Apply.
Have you installed any new programs or software recently?
I was experimenting with some registry tweaks, I downloaded a few freeware tools to test them. I think that it was regtick pro that toold me that there were restrictions on the start menu. so I removed the restrictions and the icons came back gradualy as I used programs.