I recently switched my email client from Mozilla Thunderbird 2.x to Mozilla SeaMonkey (latest) as Mozilla Thunderbird 3.x is so undesirable. Things were working quite well. I found the place to set which component of SeaMonkey it opens to on start up and selected the Mail component.

However there was one annoyance! In Firefox when a web page has a mailto: link, clicking that link would not open a new SeaMonkey email window... I would only see the SeaMonkey program flash in the lower panel within Ubuntu Gnome desktop.