Programs missing from windows xp start menu and quick launch

Hello, you might want to skip the next description and jump right to the link below, if after that you need more background information on the issue, please come back. :)

I have a problem (no, duh :) ): I was just surfing teh internets with Opera last night when it crashed from opening a site (happens normally from time to time). I waited for it to restart (as it usually does) but it didn't, so I opened it again, opened the same site and it was fine (also nromal) but then a little while later it crashed from another site and this time my system started spamming system error messages like crazy. There were several types but I didn't wait long before I restarted the computer, trying to start it normally - my desktop icons were gone, my quick launch was gone and after a couple of seconds of normal loading programs started to close like alcohol stores during the great depression, so I restarted again in safe mode, backed up all my desktop and other important files and found out all information on my hard drives was intact (including the files on my desktop), again no icons and etc. , since I haven't done anything besides surfingh teh internets I thought I had a virus of something (even though I have firewall, anivirius and anispyware) so I ran my Spybot Search & Destroy and my NOD32 in an attempt to purge the interloper. Spybot found something little, tiny and evil within Windows explorer and I told him to eliminate it. Since I couldn't wait much longer I shut down NOD32 and turned my PC off. The next day (today) I started in safe mode again, and this time there were icons on my desktop (yay!), and let it scan for longer, still I couldn't wait for it to finish all the way (even though I left it for 2 hours) and decided to try my chances with a normal start. So now I have desktop icons, but some of my user settings are messed up - no quick launch, most of my program folders in start menu are empty (even though all programs are well acounted for and working fine) - I don't even have paint or calculator!, Opera asked me if I want it to be my default browser, and it has been for three years, the "hide inactive icons" option of my taskbar was unchecked (before it was checked), I notice I have a few less running programs in my system tray and my windows explorer view settings are a little off.

I saw this topic: and, yes - it is almost exactly the same. Only I always have "Show hidden files and folders" checked and there are no files in that "C:\Documents and Settings\Administrator\Local Settings\Temp\smtmp\" only empty folders ("1" and "2", with "2" being completely devoid of anything). I ran a search on my entire computer and there is no other "smtmp" folder anywhere.

Currently NOD32 is scanning in-depth and I seem to remember when I first started Spybot (on my first safe-mode) that he said there were 400+ temporary files (Spybot always scans for present temporary files before conducting a malware scan in order to increase scanning speed) and I told him to delete them. I am mentioning this anyway, even tough I do not think he deleted the icons 'n' such, since it was after a restart. They were probably leftover from all the backing-up of data I did then.

I would be very grateful for any assistance, thank you!
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More about programs missing windows start menu quick launch
  1. Delete all temporary files in all user folders like Default, All Users, <your user name> indiscriminantly, especially the .exe executable files found there, don't forget C:\windows\temp. This is a bad rootkit usually known as "windows antivirus" or "windows security". Run msconfig and make sure virus not loading on boot or as service (hide Microsoft). There are applications out there that would restore Accessories and Admin Tools folders to original, restore windows to previous state you will find does not work. You can place a shortcut to everything in Program Files folder to your desktop. I believe MS Office has a way to restore shortcuts through repair install. It's a patch until you eventually re-install windows. Scan all backups made, as you did the backups with the virus on.
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