Not sure if this will help, but the last time I saw a problem such as yours it actually had more to do with the previous anti virus product that was installed on the machine, then MSE. Do you recall what antivirus product you were using prior to MSE?
It may help if you download the proprietary removal tool for that specific product and run it to see if it can remove any problem remnants of the former product.
The only other thing that I can think of that may get you over the hump is, if you were running MSE v1, you might try downloading and attempting to install the latest MSE Beta for version 2 here
https://connect.microsoft.com/Downloads/Downloads.aspx?SiteID=861
you'll need a live id, it's relatively painless and straight forward, might be worth a try.