Hey Taz,
I'm glad to see the code was of some help to you. Messenger Plus! does search for Messenger windows and it actually also searches for the systray one. However, in order to prevent everythign to be initialised too soon or for no reason, when the systray window is created, Messenger Plus! waits a couple of seconds for one of the visible windows of Messenger to be created. If none is created before 5 or 6 seconds, everything is initialised and the plugins are loaded at the same time.
I understand this may not be the best thing for your plugin but for everything else, that's one of the things that insures that Messenger Plus! does not causes problems with Messenger
.