You certainly can't rule out any possible malware. New Computer Virus Can Override Anti-Virus
Typically a mouse virus or better yet adware or trojan downloader works more like a browser hijacker while the problem there sounds more like missing system files or corrupted system files to an extend beyond what the SFC could do for you.
One thing I could suggest here would be the VIPRE Rescue Program
which runs out of a temp folder without any installation. Once you have it downloaded boot up in safe mode and drag it onto the desktop from the folder you download it to. That will create a shortcut for it there.
It won't run in safe mode so you then will reboot up as you would normally but to simply double click on the exe file. That will unpack itself by then creating a new temp folder you can delete later to run out of and start the ball game from there. Despite being booted in Windows the VRP runs as a stand alone live tool.
What that will do is root out any traces of malware as well as get Windows back running again if any infection is found. It won't sweep the entire drive however just restore the OS functionality.
If you are not seeing any malware then you may simply have to elect the repair install or even full clean install if you are unable to find a solution. That still can't be ruled out however since I-Worm type viruses are known to trash system files as well as self replicate themselves through your email contacts to spread even further.
Once any Windows installation becomes too problematic it's usually best to plan a clean install to resolve everything. That is with or without any malwares or virus concerns simply from the extent while often a virus or rogue ware will end trashing the OS anyways.