Ok now THIS has really been an annoying problem so tonight I decided to find the answer to fixing the problem. Every single time I've opened up Messenger for the last couple weeks it said I had an invitation in my Windows Live account to view. The thing is that I never did. I looked through all the notification options and eventually unchecked them all. I did this for both Messenger and my Windows Live Space or page. It STILL was telling me I had an invitation waiting for me in Messenger when I would open it.
Well I found the fix and here it is!
Close Messenger first.
Go toUser\<User>\AppData\Local\Microsoft\Windows Live Contactsand remove everything there. Just delete it all because as far as I could tell when I logged back in I didn't love the conversation history's or anything. Open Messenger back up and Viola! No more annoying invitation notification. Mystery solved. 