There seems to be issues with how long the Balloon tip takes to vanish even if you set a low duration (as show to be 3 seconds in the code below).

notifyIconMain.ShowBalloonTip(3000, "XYZ...", MyVar, ToolTipIcon.Info);

For more information see my blog post on this subject: http://blog.lyalin.com/2007/12/showballoontip-problem-in-notifyicon.html

Since Microsoft have neglected to provide this essential information, I'll do it for them. Ensure HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced\EnableBalloonTips is set to 1 if your balloon tips don't show up at all.