Ah, that explains it, my Vista install had gone through multiple versions with saved configs, which would explain why I had never seen it minimize to tray before... I can confirm that this is the case and that it functions normally after showing the tray icon.
One other minor bit, Windows complained about mIRC needing agentctl.dll which is no longer available, I'm not sure what this would effect, but the error hasn't recurred since [or windows is hiding it for me].