*raises a hand* Uhm did you already have another Antivirus WITH MSE installed on the computer? If so that was the root cause, you can only have ONE Antivirus on a computer at a time. If you didn't have TWO Antivirus running, only MSE, well you just made your computer vulnerable and you need a Antivirus installed asap (recommend AVAST! ) .
From my gloss over those errors, the first supposition was the HDD (where the files are stored) is corrupt or bad sectors. As you said your computer comes up fine during scans, but you said you messed with Services, I believe you may have turned off interdependent services by mistake. I would stop everything you're doing, open services on one side of the screen then open this site (http://www.blackviper.com/service-configurations/black-vipers-windows-7-service-pack-1-service-configurations/)
on the other side, and take his recommended settings before doing anything else then reboot. If things get 'wonky' again from making these changes, then I think Windows in itself maybe corrupt (which goes back to the system repair option to clear things up) or there has Malware (not a virus) messing in the background that MSE was trying (badly) to fight off and you just took away the protection. Run MalwareBytes on your computer and see if that detects anything (Malware is different then Viruses, and 'fake' things to socially engineer you to do things incorrectly and hijack your computer).