I don't use any flight sim at this time but doubt that the sim upgrade has anything to do with it unless you got the upgrade from a web site other than real flight.
Try booting in "SAFE" Mode. If you can get to safe mode you can temporaly un-install the up grade or the whole sim program and then see if the computer will start normally. BUT, first I would suggest you goto the microsoft web site and download "Microsoft Essentials" and run that to see if you have been infected by a virus. Another tool is Mal-wear bytes and Ad-Aware. If you find a bug you can remove it with these tools. Then do a defrag on the system. Just doing a restore will not remove any virus or th's from the system.