You might run "sfc /scannow" in safe mode. That's the 'system file checker', it should be able to find any files that have been corrupted.
Also you might try installing Microsoft's Security Essentials (it's free!) from (http://windows.microsoft.com/en-us/windows/security-essentials-download). My dad had malware bytes installed on his computer by a 3rd party, and it didn't detect the adware that had taken over his browser and desktop -- but installed MSE, and it discovered it on the 1st scan.
As a last resort, you might try an "inplace" upgrade by putting in your windows-install CD and doing an "upgrade" to the same version you already have (i.e. professional -> professional, home->home...etc). This will re-install the original files and proceed to do download updates.
It also could be a hardware related issue -- like I can reproduce such symptoms if I saturate my 10Gb network connection -- the OS get sluggish and has problems bringing up the login screen -- it will eventually (usually), but if too many interrupts are coming in or something is running which slows down your computer, it can cause such symptoms.
A good utility to see what is running on your system (and kill it if necessary, is "Process Hacker" on "Sourceforge". Much better than task manager or "Process Explorer" from the sysinternals-microsoft site. When Process Explorer couldn't
kill or delete the "adware" process that had infected my dad's
computer, Process Hacker was able to override it's protections and allow it's removal. You can download it from http://processhacker.sourceforge.net/ .