This issue has been bothering me for some time now and I have finally figured it out. Every time I check my hotmail, live emails, IE automatically starts MSN Messenger. It does not log me in, just opens it and sits there and I have to close it every single time.
Here are the steps to disable it:
1. Open Internet Explorer
2. Under Tools > Manage Add-ons, highlight “Windows Live” and click the Disable button (If Windows Live does not appear, change the Show drop-down to All add-ons)
3. Close Internet Explorer and login to hotmail again. Messenger should not launch anymore. It will show you an alert in IE about an add-on being disabled, just ignore it.