If you really have that many files that cannot be repaired, you must have something really messing with your system. If you do not have some idea what might be going on, perhaps davehc is correct about the virus. Malwarebytes is normally pretty good, but not guaranteed.
I would suggest you do a Repair Install of Windows 7. You will be able to keep your data and installed programs, but the Windows part will be redone.
A Repair Install is where you start an update from within your Win 7 install and install over your current install. I would back up everything I could, but keep in mind to try to not use it if you do not have to.
If that many files are messed up, the problem may come back. I cannot think of a reason why that many files could not be verified.
I might even want to get a new hard drive and do a temporary Win 7 install to see if it would stay clean.