Are you still getting that message as , strangely , it does seem to have conincided with the
recent update for microsoft
http://support.microsoft.com/kb/890830
Have you considered that and did you take that on with your Patches?
Of interest, has your Avast program stopped running at all ?
Well, that link above points to the mrt.exe file, which Microsoft offers with every monthly update on Tuesday. As this is optional (can be declined by the admin user) and is deployed by Microsoft to catch and remove unwanted malware in all currently supported operating systems, it would seem as if you may have had a bout with some malware on your system, and consequently may be blaming Microsoft for issues originating from the presence of malware that this tool detected and removed after running this tool?
Malware not completely removed will cause operating issues that seem random and are difficult to pin down with any certainty as to what is causing what. It isn't likely that the Microsoft Windows Malicious Software Removal Tool is the cause of any issues you are seeing.
Start a new topic in viruses and worm section and ask for help from essexboy for your system, I say.