I took a look at the desktop.ini file in the Programs directory, but it was only one line long. I didn't know what to make of it. But I did think of a workaround. I created a new folder with a different name in the Programs folder. Then, I copied the icon files over to the new folder with the command line. I still don't know what is causing the problem, or how to fix it directly, but the workaround has taken care of my problem. I can see the icons in the start menu now. (Just hope it doesn't happen again.)