I got a pop-up message that appered to be from Microsoft Security Essentials, but it seemed to mess with my system. Was it a virus?
Yes, that was probably a virus to trick you to install another application. Microsoft's software doesn't display unusual pop-ups. In order to avoid such situations, you should install antivirus software and try to reconsider your actions if any malicious pop-ups will appear on your screen.
You can download other antivirus software from the following location : http://software.informer.com/search/antivirus