Half of Desktop icons dissappeared...

So I just upgraded my home-made vista home premium machine to windows 7 home premium. When I got into windows 7 for the first time, everything was as expected (only a couple of incompatible programs but nbd). My desktops icons were all still there and like I mentioned most of my programs were still running just fine. Then, late at night when I was fooling around with some files (either deleting stuff or trying to update drivers or something) I noticed my desktop refreshed and came back with nearly half the icons it had before. When I searched for those programs that the deleted icons executed, they were still in my computer but some of there icons had been changed to the windows default one, which sorta looks like a page with the top right corner bent in and a little M$ Window opened. You guys know what I mean.

So I was wondering if there was anyway to troubleshoot this problem or if anybody has any idea what happened. PLEASE HELP!