Once you're up and running, run the command prompt in admin mode, see here. Type sfc /scannow, or copy and paste, then press enter. Go and make a cup of coffee as it can take some time. If you have errors that can't be fixed run sfc (system file checker) another couple of times.
Have you removed any virus or malware that has created this state or have you run any security software at all? It sounds as the OS is damaged.