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It is my opinion that the update was not from MSE, but from a rogue (a virus that was made to look like MSE). When you updated you installed the virus. The cause is truly not important, but rather what we will do to solve the problem.
See if you can get to system restore in safe mode. If you can, go back a few days before the upadate.
System Restore - How to

Sounds like scareware to me. Could this be what you are experiencing? New Scareware Displays Fake Microsoft Security Essentials Alerts - Softpedia

Rogue Security Software | Rogue Security Software Removal

On the other hand if MSE was out of date then you might have had viruses on your computer that you didn't know about which is why you must have your anti-virus/anti-spyware check for updates at least weekly. If you really are infected then I wouldn't revert to a restore point because it can also be infected. You will first need to determine whether or not what you are seeing is legit. Is it wanting you to buy something? If so then it probably is scareware and more than likely buying it will only make your wallet lighter. A screenshot might help us advise you further.