Yesterday (May 13, 2011) I was struck by the MS REMOVAL TOOL malware infection. I followed the guide you posted here http://www.bleepingcomputer.com/virus-removal/remove-ms-removal-tool
to the letter with one exception -- I did not find an unauthorized proxy server connection to disable because one was not displayed there.
After completing all the steps, I found most of my desktop folders and files were still hidden from view. I ran the UNHIDE program, because it worked for me a couple of weeks ago when I had the similar System Tool malware infection. UNHIDE seemed to work well this time too, until I attempted to do a System Restore today. I wanted to do a System Restore to an earlier date in an attempt to make certain that my PC was in an uninfected state.
When I followed the path to Start|All Programs|Accessories|System Tools I found that System Restore is no longer available to me. Neither are Disk Defragment and Disc Cleanup which are usually in that list of System Tools.
In fact, almost all my Start Menu programs are hidden or their folders are showing (Empty)
As I am watching GMER run, I can see that many of these programs are still on my system because GMER is scanning its components and support files. Both MalwayrBytes abd Microsoft Security Essentials show my system clean at this point. But given that I cannot find my installed programs or do a System Restore, I am certain that this PC is either still infected or permanently damaged.
What are my options? I am unsure whether to post my logs. Your users guide says to, but the rules for this forum say not to. I will appreciate any help you can offer. Thank you.