i had this too, just go to tools > options >sounds and alerts and uncheck "display alerts when contacts come online"
(and enable that option with plus!, in plus preferences > notifications > popup defults (the box at the bottom under "custom signin notifications") make sure you enable notifications for your contacts though or you will get none
i don't know why, but it is only a problem with msn's signin notification option and does not re-occur with plus' notifications
/ 
gif 
