I just found the solution I think. I had installed Hiyo and think that was when it started auto opening, seems Hiyo was in my autostarts. I unchecked it and tonight, messenger did not start on boot and my entire boot up went faster. Whew, so anyone with same issue, check that other componants of live messenger are not set to start on boot.
I found and disabled Hiyo from autostart with the program Startupcop.
http://www.pcmag.com/article2/0,4149,2173,00.asp