Desktop items & start menu items missing/hidden after virus

I originally posted this on the software forum but no one has replied after a couple days so I thought I would try it over here:

Okay, so my computer got infected and I downloaded paid versions of SuperAntiSpyware & Avira Antivirus and ran them plus a bunch of others from the Malware thread and was able to clean up my system but a bunch of my shortcuts on my desktop disappeared and my Start Menu is messed up. I was able to manually put a few of my shortcuts back on to my desktop but they showed up dimmed like they were hidden. I went and double checked in Folder Options to show hidden files and that was already selected. I downloaded and ran UnHide and all it did was make the dimmed shortcuts turn back normal but did not put all the others back. Also, if I try to open c:/Documents and Settings it pops up that it is not accessible and access is denied. The folder is also dimmed like it is hidden.

So at this point I don't know what else to do. :confused

Running Vista 64-bit

TIA

 

Okay - I figured it out, lol. I read info at http://www.realgeek.com/forums/why-cant-i-access-my-start-menu-etc-474189.html I manually replaced all my shortcuts and now I'm set. Start Menu is back to normal as well.

Thought I'd post back in case someone else has this problem later on.

 

Apologies to both of you; I try to pick up any threads in Software if I feel there's a chance of malware involvement, or of ruling it out. That was one that slipped past me, despite the obvious title.