Have you tried several tools to make sure you're clean?
I just dealt with something like this over the weekend on a client system and found the MSE was interfering with the process.
1st: as many many of us say, the best bet is to save your valuables, zero-nuke the hard drive, and reinstall.
That said, I would update malwarebytes definitions IF you can do so safely, and also download & install 'superantispyware' or spybot S&D if you have some expertise... the latter is complicated.
then I would reboot, F8, Safe Mode no networking, and make darn sure when the system comes up that MSMPeng.exe is NOT RUNNING. stop it, disable it... whatever.
then run malwarebytes full scan and see what it finds. take the remediation steps. then run one of the others.
Rootkits can/will damage OS files.
Curing rootkits, droppers, etc can & will damage OS files sometimes.
My experience over many, many infections/cleanups is that one ends up spending less time, and getting far better results, but wiping/reloading but make sure the wipe is a Secure Wipe, not a delete/reformat.