You can find a lot of good documentation in The Linux Documenation Project http://www.tldp.org/ Can you be more specific about what exactly happens when you boot your computer?
I don't have this problem. Just tested it.Started Y! Messenger and firstly got new mail notification, so read new messages, closed Y! messenger and started it again. This time got no new email notification.I'm using Y! Messenger 8.1.0.402 on Windows XP.