When I restart my computer and login and everything loads the message isn't there, but after a while the message with show up and I have to restart my computer to make it temporarily go away, so why am I getting that message and how can I make it so it doesn't reappear.
Have you tried re-activating? Have you called MS to explain situation? Microsoft usually will help you get it re-activated after answering a few questions
The actual message you get might be important. There are several sites that relate to your situation but I will only show two. The first link is for validating your install. It might take ActiveX or some downloaded component. The second link is for a situation where you get a specific error message. Maybe one will help. The updates question from jdmcertified is important, because part of the checking is done through the Windows Update process.
Genuine Windows customers get a complimentary subscription to Microsoft Security Essentials, the award-winning, antivirus software that helps you protect your PC.
I just used IE to check, and after allowing the ActiveX to run, I see the same as you. So I would say it is genuine, but do not know why the messages are appearing without some type of error message.